Provided by: vsearch_2.27.0-1_amd64 
NAME
vsearch — a versatile open-source tool for microbiome analysis, including chimera detection, clustering,
dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting,
pairwise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic
classification of amplicon sequences for metagenomics, genomics, and population genetics.
SYNOPSIS
Chimera detection:
vsearch (--uchime_denovo | --uchime2_denovo | --uchime3_denovo) fastafile (--chimeras |
--nonchimeras | --uchimealns | --uchimeout) outputfile [options]
vsearch --uchime_ref fastafile (--chimeras | --nonchimeras | --uchimealns | --uchimeout)
outputfile --db fastafile [options]
Clustering:
vsearch (--cluster_fast | --cluster_size | --cluster_smallmem | --cluster_unoise) fastafile
(--alnout | --biomout | --blast6out | --centroids | --clusters | --mothur_shared_out | --msaout |
--otutabout | --profile | --samout | --uc | --userout) outputfile --id real [options]
Dereplication and rereplication:
vsearch --fastx_uniques (fastafile | fastqfile) (--fastaout | --fastqout | --tabbedout | --uc)
outputfile [options]
vsearch (--derep_fulllength | --derep_id | --derep_prefix) fastafile (--output | --uc) outputfile
[options]
vsearch --derep_smallmem (fastafile | fastqfile) --fastaout outputfile [options]
vsearch --rereplicate fastafile --output outputfile [options]
Extraction of sequences:
vsearch --fastx_getseq fastafile (--fastaout | --fastqout | --notmatched | --notmatchedfq)
outputfile --label label [options]
vsearch --fastx_getseqs fastafile (--fastaout | --fastqout | --notmatched | --notmatchedfq)
outputfile (--label label --labels labelfile | --label_word label | --label_words labelfile)
[options]
vsearch --fastx_getsubseq fastafile (--fastaout | --fastqout | --notmatched | --notmatchedfq)
outputfile --label label [--subseq_start position] [--subseq_end position] [options]
FASTA/FASTQ/SFF file processing:
vsearch --fasta2fastq fastqfile --fastqout outputfile [options]
vsearch --fastq_chars fastqfile [options]
vsearch --fastq_convert fastqfile --fastqout outputfile [options]
vsearch (--fastq_eestats | --fastq_eestats2) fastqfile --output outputfile [options]
vsearch --fastq_filter fastqfile [--reverse fastqfile] (--fastaout | --fastaout_discarded |
--fastqout | --fastqout_discarded --fastaout_rev | --fastaout_discarded_rev | --fastqout_rev |
--fastqout_discarded_rev) outputfile [options]
vsearch --fastq_join fastqfile --reverse fastqfile (--fastaout | --fastqout) outputfile [options]
vsearch --fastq_mergepairs fastqfile --reverse fastqfile (--fastaout | --fastqout |
--fastaout_notmerged_fwd | --fastaout_notmerged_rev | --fastqout_notmerged_fwd |
--fastqout_notmerged_rev | --eetabbedout) outputfile [options]
vsearch --fastq_stats fastqfile [--log logfile] [options]
vsearch --fastx_filter inputfile [--reverse inputfile] (--fastaout | --fastaout_discarded |
--fastqout | --fastqout_discarded --fastaout_rev | --fastaout_discarded_rev | --fastqout_rev |
--fastqout_discarded_rev) outputfile [options]
vsearch --fastx_revcomp inputfile (--fastaout | --fastqout) outputfile [options]
vsearch --sff_convert sff-file --fastqout outputfile [options]
Masking:
vsearch --fastx_mask fastxfile (--fastaout | --fastqout) outputfile [options]
vsearch --maskfasta fastafile --output outputfile [options]
Orienting:
vsearch --orient fastxfile --db fastxfile (--fastaout | --fastqout | --notmatched | --tabbedout)
outputfile [options]
Pairwise alignment:
vsearch --allpairs_global fastafile (--alnout | --blast6out | --matched | --notmatched | --samout
| --uc | --userout) outputfile (--acceptall | --id real) [options]
Restriction site cutting:
vsearch --cut fastafile --cut_pattern pattern (--fastaout | --fastaout_rev | --fastaout_discarded
| --fastaout_discarded_rev) outputfile [options]
Searching:
vsearch --search_exact fastafile --db fastafile (--alnout | --biomout | --blast6out |
--mothur_shared_out | --otutabout | --samout | --uc | --userout | --lcaout) outputfile [options]
vsearch --usearch_global fastafile --db fastafile (--alnout | --biomout | --blast6out |
--mothur_shared_out | --otutabout | --samout | --uc | --userout | --lcaout) outputfile --id real
[options]
Shuffling and sorting:
vsearch (--shuffle | --sortbylength | --sortbysize) fastafile --output outputfile [options]
Subsampling:
vsearch --fastx_subsample fastafile (--fastaout | --fastqout) outputfile (--sample_pct real |
--sample_size positive integer) [options]
Taxonomic classification:
vsearch --sintax fastafile --db fastafile --tabbedout outputfile [--sintax_cutoff real] [options]
UDB database handling:
vsearch --makeudb_usearch fastafile --output outputfile [options]
vsearch --udb2fasta udbfile --output outputfile [options]
vsearch (--udbinfo | --udbstats) udbfile [options]
DESCRIPTION
Environmental or clinical molecular diversity studies generate large volumes of amplicons (e.g.; SSU-rRNA
sequences) that need to be checked for chimeras, dereplicated, masked, sorted, searched, clustered or
compared to reference sequences. The aim of vsearch is to offer a all-in-one open source tool to perform
these tasks, using optimized algorithm implementations and harvesting the full potential of modern
computers, thus providing fast and accurate data processing.
Comparing nucleotide sequences is at the core of vsearch. To speed up comparisons, vsearch implements an
extremely fast Needleman-Wunsch algorithm, making use of the Streaming SIMD Extensions (SSE2) of
post-2003 x86-64 CPUs. If SSE2 instructions are not available, vsearch exits with an error message. On
Power8 CPUs it will use AltiVec/VSX/VMX instructions, and on ARMv8 CPUs it will use Neon instructions.
Memory usage increases rapidly with sequence length: for example comparing two sequences of length 1 kb
requires 8 MB of memory per thread, and comparing two 10 kb sequences requires 800 MB of memory per
thread. For comparisons involving sequences with a length product greater than 25 million (for example
two sequences of length 5 kb), vsearch uses a slower alignment method described by Hirschberg (1975) and
Myers and Miller (1988), with much smaller memory requirements.
Input
vsearch accept as input fasta or fastq files containing one or several nucleotidic entries. In fasta
files, each entry is made of a header and a sequence. The header is defined as the string comprised
between the initial '>' symbol and the first space, tab or the end of the line, unless the
--notrunclabels option is in effect, in which case the entire line is included. The header should contain
printable ascii characters (33-126). The program will terminate with a fatal error if there are
unprintable ascii characters. A warning will be issued if non-ascii characters (128-255) are encountered.
If the header matches the pattern '>[;]size=integer;label', the pattern '>label;size=integer;label', or
the pattern '>label;size=integer[;]', vsearch will interpret integer as the number of occurrences (or
abundance) of the sequence in the study. That abundance information is used or created during chimera
detection, clustering, dereplication, sorting and searching.
The sequence is defined as a string of IUPAC symbols (ACGTURYSWKMDBHVN), starting after the end of the
identifier line and ending before the next identifier line, or the file end. vsearch silently ignores
ascii characters 9 to 13, and exits with an error message if ascii characters 0 to 8, 14 to 31, '.' or
'-' are present. All other ascii or non-ascii characters are stripped and complained about in a warning
message.
In fastq files, each entry is made of sequence header starting with a symbol '@', a nucleotidic sequence
(same rules as for fasta sequences), a quality header starting with a symbol '+' and a string of ASCII
characters (offset 33 or 64), each one encoding the quality value of the corresponding position in the
nucleotidic sequence.
vsearch operations are case insensitive, except when soft masking is activated. Masking is automatically
applied during chimera detection, clustering, masking, pairwise alignment and searching. Soft masking is
specified with the options '--dbmask soft' (for searching and chimera detection with a reference) or
'--qmask soft' (for searching, de novo chimera detection, clustering and masking). When using soft
masking, lower case letters indicate masked symbols, while upper case letters indicate regular symbols.
Masked symbols are never included in the unique index words used for sequence comparisons, otherwise they
are treated as normal symbols.
When comparing sequences during chimera detection, dereplication, searching and clustering, T and U are
considered identical, regardless of their case. When aligning sequences, identical symbols will receive a
positive match score (default +2). If two symbols are not identical, their alignment result in a negative
mismatch score (default -4). Aligning a pair of symbols where at least one of them is an ambiguous symbol
(BDHKMNRSVWY) will always result in a score of zero. Alignment of two identical ambiguous symbols (for
example, R vs R) also receives a score of zero. When computing the amount of similarity by counting
matches and mismatches after alignment, ambiguous nucleotide symbols will count as matching to other
symbols if they have at least one of the nucleotides (ACGTU) they may represent in common. For example: W
will match A and T, but also any of MRVHDN. When showing alignments (for example with the --alnout
option) matches involving ambiguous symbols will be shown with a plus character (+) between them while
exact matches between non-ambiguous symbols will be shown with a vertical bar character (|).
vsearch can read data from standard files and write to standard files, but it can also read from pipes
and write to pipes! For example, multiple fasta files can be piped into vsearch for dereplication. To do
so, file names can be replaced with:
- the symbol '-', representing '/dev/stdin' for input files or '/dev/stdout' for output files
(with an exception for '--db -', see * below),
- a named pipe created with the command mkfifo,
- a process substitution '<(command)' as input or '>(command)' as output.
* --db - is not accepted, to prevent potential concurrent reads from stdin. A workaround for
advanced users is to call '--db /dev/stdin' directly.
vsearch can automatically read compressed gzip or bzip2 files if the appropriate libraries are present
during the compilation. vsearch can also read pipes streaming compressed gzip or bzip2 data if the
options --gzip_decompress or --bzip2_decompress are selected. When reading from a pipe, the progress
indicator is not updated.
Options
vsearch recognizes a large number of command-line commands and options. For easier navigation, options
are grouped below by theme (chimera detection, clustering, dereplication and rereplication, FASTA/FASTQ
file processing, masking, pairwise alignment, searching, shuffling, sorting, and subsampling). We start
with the general options that apply to all themes. Options start with a double dash (--). A single dash
(-) may also be used, except on NetBSD systems. Option names may be shortened as long as they are not
ambiguous (e.g. --derep_f).
Help and version commands:
--help --h
Display help text with brief information about all commands and options.
--version --v
Output version information and a citation for the VSEARCH publication. Show the status of
the support for gzip- and bzip2-compressed input files.
General options:
--bzip2_decompress
When reading from a pipe streaming bzip2-compressed data, decompress the data. This
option is not needed when reading from a standard bzip2-compressed file.
--fasta_width positive integer
Fasta files produced by vsearch are wrapped (sequences are written on lines of integer
nucleotides, 80 by default). Set the value to zero to eliminate the wrapping.
--gzip_decompress
When reading from a pipe streaming gzip-compressed data, decompress the data. This option
is not needed when reading from a standard gzip-compressed file.
--label_suffix string
When writing FASTA or FASTQ files, add the suffix string to sequence headers.
--log filename
Write messages to the specified log file. Information written includes program version,
amount of memory available, number of cores and command line options, and if need be,
informational messages, warnings and fatal errors. The start and finish times are also
recorded as well as the elapsed time and the maximum amount of memory consumed. The
different vsearch commands can also write additional information to the log file.
--maxseqlength positive integer
All vsearch operations discard sequences longer than integer (50,000 nucleotides by
default).
--minseqlength positive integer
All vsearch operations discard sequences shorter than integer: 1 nucleotide by default
for sorting or shuffling, 32 nucleotides for clustering and dereplication as well as the
commands --makeudb_usearch, --sintax, and --usearch_global.
--no_progress
Do not show the gradually increasing progress indicator.
--notrunclabels
Do not truncate sequence labels at first space or tab, but use the full header in output
files. Turned off by default for all commands except the sintax command.
--quiet Suppress all messages to stdout and stderr except for warnings and fatal error messages.
--sample string
When writing FASTA or FASTQ files, add the the given sample identifier string to sequence
headers. For instance, if the given string is ABC, the text ";sample=ABC" will be added
to the header.
--threads positive integer
Number of computation threads to use (1 to 1024). The number of threads should be less
than or equal to the number of available CPU cores. The default is to use all available
resources and to launch one thread per core. The following commands are multi-threaded:
allpairs_global, cluster_fast, cluster_size, cluster_smallmem, cluster_unoise,
fastq_mergepairs, fastx_mask, maskfasta, search_exact, sintax, uchime_ref, and
usearch_global. Only one thread is used for the other commands.
Chimera detection options:
Chimera detection is based on a scoring function controlled by five options (--dn, --mindiffs,
--mindiv, --minh, --xn). Sequences are first sorted by decreasing abundance, if available, and
compared on their plus strand only (case insensitive).
Input sequences are masked as specified with the --qmask and --hardmask options. Masking of the
database for reference based chimera detection is specified with the --dbmask option.
In de novo mode, input fasta file must present abundance annotations (i.e. a pattern
[;]size=integer[;] in the fasta header). Input order matters for chimera detection, so we
recommend to sort sequences by decreasing abundance (default of --derep_fulllength command). If
your sequence set needs to be sorted, please see the --sortbysize command in the sorting section.
--abskew real
When using --uchime_denovo, the abundance skew is used to distinguish in a three-way
alignment which sequence is the chimera and which are the parents. The assumption is that
chimeras appear later in the PCR amplification process and are therefore less abundant
than their parents. For --uchime3_denovo the default value is 16.0. For the other
commands, the default value is 2.0, which means that the parents should be at least 2
times more abundant than their chimera. Any positive value equal or greater than 1.0 can
be used.
--alignwidth positive integer
When using --uchimealns, set the width of the three-way alignments (80 nucleotides by
default). Set to zero to eliminate wrapping.
--borderline filename
Output borderline chimeric sequences to filename, in fasta format. Borderline chimeric
sequences are sequences that have a high enough score but which are not sufficiently
different from their closest parent.
--chimeras filename
Output chimeric sequences to filename, in fasta format. Output order may vary when using
multiple threads.
--db filename
When using --uchime_ref, detect chimeras using the reference sequences contained in
filename. Reference sequences are assumed to be chimera-free. Chimeras cannot be detected
if their parents, or sufficiently close relatives, are not present in the database. The
file name must refer to a FASTA file or to a UDB file. If a UDB file is used, it should
be created using the --makeudb_usearch command with the --dbmask dust option.
--dn strictly positive real number
pseudo-count prior on the number of no votes, corresponding to the parameter n in the
chimera scoring function (default value is 1.4). Increasing --dn reduces the likelihood
of tagging a sequence as a chimera (less false positives, but also more false negatives).
--fasta_score
Add the chimera score to the headers in the fasta output files for chimeras, non-chimeras
and borderline sequences, using the format ';uchime_denovo=float;'.
--lengthout
Write sequence length information to the output files in FASTA format by adding a
";length=integer" attribute in the header.
--mindiffs positive integer
Minimum number of differences per segment (default value is 3). The parameter is ignored
with --uchime2_denovo and --uchime3_denovo.
--mindiv real
Minimum divergence from closest parent (default value is 0.8). The parameter is ignored
with --uchime2_denovo and --uchime3_denovo.
--minh real
Minimum score (h). Increasing this value tends to reduce the number of false positives
and to decrease sensitivity. Default value is 0.28, and values ranging from 0.0 to 1.0
included are accepted. The parameter is ignored with --uchime2_denovo and
--uchime3_denovo.
--nonchimeras filename
Output non-chimeric sequences to filename, in fasta format. Output order may vary when
using multiple threads.
--relabel string
Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the
new headers. Use --sizeout to conserve the abundance annotations.
--relabel_keep
When relabelling, keep the old identifier in the header after a space.
--relabel_md5
Relabel sequences using the MD5 message digest algorithm applied to each sequence. Former
sequence headers are discarded. The sequence is converted to upper case and each 'U' is
replaced by a 'T' before computation of the digest. The MD5 digest is a cryptographic
hash function designed to minimize the probability that two different inputs give the
same output, even for very similar, but non-identical inputs. Still, there is a very
small, but non-zero, probability that two different inputs give the same digest (i.e. a
collision). MD5 generates a 128-bit (16-byte) digest that is represented by 16
hexadecimal numbers (using 32 symbols among 0123456789abcdef). Use --sizeout to conserve
the abundance annotations.
--relabel_self
Relabel sequences using each sequence itself as a label.
--relabel_sha1
Relabel sequences using the SHA1 message digest algorithm applied to each sequence. It is
similar to the --relabel_md5 option but uses the SHA1 algorithm instead of the MD5
algorithm. SHA1 generates a 160-bit (20-byte) digest that is represented by 20
hexadecimal numbers (40 symbols). The probability of a collision (two non-identical
sequences resulting in the same digest) is smaller for the SHA1 algorithm than it is for
the MD5 algorithm.
--self When using --uchime_ref, ignore a reference sequence when its label matches the label of
the query sequence (useful to estimate false-positive rate in reference sequences).
--selfid When using --uchime_ref, ignore a reference sequence when its nucleotide sequence is
strictly identical to the nucleotidic sequence of the query.
--sizein In de novo mode, abundance annotations (pattern '[>;]size=integer[;]') present in
sequence headers are taken into account by default (--sizein is always implied). This
option is ignored by --uchime_ref.
--sizeout
When relabelling, add abundance annotations to fasta headers (using the format
';size=integer;').
--uchime_denovo filename
Detect chimeras present in the fasta-formatted filename, without external references
(i.e. de novo). Automatically sort the sequences in filename by decreasing abundance
beforehand (see the sorting section for details). Multithreading is not supported.
--uchime2_denovo filename
Detect chimeras present in the fasta-formatted filename, using the UCHIME2 algorithm.
This algorithm is designed for denoised amplicons (see --cluster_unoise). Automatically
sort the sequences in filename by decreasing abundance beforehand (see the sorting
section for details). Multithreading is not supported.
--uchime3_denovo filename
Detect chimeras present in the fasta-formatted filename, using the UCHIME2 algorithm. The
only difference from --uchime2_denovo is that the default minimum abundance skew
(--abskew) is set to 16.0 rather than 2.0.
--uchime_ref filename
Detect chimeras present in the fasta-formatted filename by comparing them with reference
sequences (option --db). Multithreading is supported.
--uchimealns filename
Write the three-way global alignments (parentA, parentB, chimera) to filename using a
human-readable format. Use --alignwidth to modify alignment length. Output order may vary
when using multiple threads. All sequences are converted to upper case before alignment.
Lower case letters indicate disagreement in the alignment.
--uchimeout filename
Write chimera detection results to filename using a 18-field, tab-separated uchime-like
format. Use --uchimeout5 to use a format compatible with usearch v5 and earlier versions.
Rows output order may vary when using multiple threads.
1. score: higher score means a more likely chimeric alignment.
2. Q: query sequence label.
3. A: parent A sequence label.
4. B: parent B sequence label.
5. T: top parent sequence label (i.e. parent most similar to the query). That
field is removed when using --uchimeout5.
6. idQM: percentage of similarity of query (Q) and model (M) constructed as a
part of parent A and a part of parent B.
7. idQA: percentage of similarity of query (Q) and parent A.
8. idQB: percentage of similarity of query (Q) and parent B.
9. idAB: percentage of similarity of parent A and parent B.
10. idQT: percentage of similarity of query (Q) and top parent (T).
11. LY: yes votes in the left part of the model.
12. LN: no votes in the left part of the model.
13. LA: abstain votes in the left part of the model.
14. RY: yes votes in the right part of the model.
15. RN: no votes in the right part of the model.
16. RA: abstain votes in the right part of the model.
17. div: divergence, defined as (idQM - idQT).
18. YN: query is chimeric (Y), or not (N), or is a borderline case (?).
--uchimeout5
When using --uchimeout, write chimera detection results using a 17-field, tab-separated
uchime-like format (drop the 5th field of --uchimeout), compatible with usearch version 5
and earlier versions.
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
--xn strictly positive real number
weight of no votes, corresponding to the parameter beta in the scoring function (default
value is 8.0). Increasing --xn reduces the likelihood of tagging a sequence as a chimera
(less false positives, but also more false negatives).
--xsize Strip abundance information from the headers when writing the output file.
Clustering options:
vsearch implements a single-pass, greedy centroid-based clustering algorithm, similar to the
algorithms implemented in usearch, DNAclust and sumaclust for example. Important parameters are
the global clustering threshold (--id) and the pairwise identity definition (--iddef).
Input sequences are masked as specified with the --qmask and --hardmask options.
--biomout filename
Generate an OTU table in the biom version 1.0 JSON file format as specified at (link)
⟨https://biom-format.org/documentation/format_versions/biom-1.0.html⟩ <https://biom-
format.org/documentation/format_versions/biom-1.0.html>. The format describes how to
store a sparse matrix containing the abundances of the OTUs in the different samples.
This format is much more efficient than the classic and mothur OTU table formats
available with the --otutabout and --mothur_shared_out options, respectively, and is
recommended at least for large tables. The OTUs are represented by the cluster centroids.
Taxonomy information will be included for the OTUs if available. Sample identifiers will
be extracted from the headers of all sequences in the input file. If the header contains
';sample=abc123;' or ';barcodelabel=abc123;' or a similar string somewhere, then the
given sample identifier (here 'abc123') will be used. The semicolon is not mandatory at
the beginning or end of the header. The sample identifier may contain any printable
character except semicolons. If no such sample label is found, the identifier in the
initial part of the header will be used, but only letters, digits and underscores are
allowed. OTU identifiers will be extracted from the headers of the cluster centroid
sequences. If the header contains ';otu=def789;' or a similar string somewhere, then the
given OTU identifier (here 'def789') will be used. The semicolon is not mandatory at the
beginning or end of the header. The OTU identifier may contain any printable character
except semicolons. If no such OTU label is found, the identifier in the initial part of
the header will be used, and all characters except semicolons are allowed. Alternatively,
OTU identifiers can be generated using the relabelling options (--relabel,
--relabel_self, --relabel_sha1, or --relabel_md5). Taxonomy information, if present, will
also be extracted from the headers of the centroid sequences. If the header contains
';tax=Homo_sapiens;' or a similar string somewhere, then the given taxonomy information
(here 'Homo_sapiens') will be used. The semicolon is not mandatory at the beginning or
end of the header. The taxonomy information may contain any printable character except
semicolons. If an OTU table in the biom version 2.1 HDF5 file format is required, the
biom utility may be used as described at (link) ⟨https://biom-format.org/documentation/
biom_conversion.html⟩ <https://biom-format.org/documentation/biom_conversion.html>.
--centroids filename
Output cluster centroid sequences to filename, in fasta format. The centroid is the
sequence that seeded the cluster (i.e. the first sequence of the cluster).
--clusterout_id
Add cluster identifier information to the output files when using the --centroids,
--consout and --profile options.
--clusterout_sort
Sort some output files by decreasing abundance instead of input order. It applies to the
--consout, --msaout, --profile, --centroids, and --uc options. For --uc, the sorting
applies only to the centroid information part (the C lines).
--cluster_fast filename
Clusterize the fasta sequences in filename, automatically sort by decreasing sequence
length beforehand.
--cluster_size filename
Clusterize the fasta sequences in filename, automatically sort by decreasing sequence
abundance beforehand.
--cluster_smallmem filename
Clusterize the fasta sequences in filename without automatically modifying their order
beforehand. Sequence are expected to be sorted by decreasing sequence length, unless
--usersort is used.
--cluster_unoise filename
Perform denoising of the fasta sequences in filename according to the UNOISE version 3
algorithm by Robert Edgar, but without the de novo chimera removal step, which may be
performed afterwards with --uchime3_denovo. The options --minsize (default 8) and
--unoise_alpha (default 2.0) may be specified. In the this algorithm, clustering of
sequences depend on both the sequence distance and the abundance ratio. The abundance
ratio (skew) is the abundance of a new sequence divided by the abundance of the centroid
sequence. This skew must not be larger than beta if the sequences should be clustered
together. Beta is calculated as 2 raised to the power of minus 1 minus alpha times the
sequence distance. The sequence distance used is the number of mismatches in the
alignment, ignoring gaps. This means that the abundance must be exponentially lower as
the distance increases from the centroid for a new sequence to be included in the
cluster. Nearer sequences with higher abundances will form their own new clusters.
--clusters string
Output each cluster to a separate fasta file using the prefix string and a ticker (0, 1,
2, etc.) to construct the path and filenames.
--consout filename
Output cluster consensus sequences to filename. For each cluster, a center-star multiple
sequence alignment is computed with the centroid as the center, using a fast algorithm
(not accurate when using low pairwise identity thresholds). A consensus sequence is
constructed by taking the majority symbol (nucleotide or gap) from each column of the
alignment. Columns containing a majority of gaps are skipped, except for terminal gaps.
If the --sizein option is specified, sequence abundances will be taken into account.
--cons_truncate
This command is ignored. A warning is issued.
--id real
Do not add the target to the cluster if the pairwise identity with the centroid is lower
than real (value ranging from 0.0 to 1.0 included). The pairwise identity is defined as
the number of (matching columns) / (alignment length - terminal gaps). That definition
can be modified by --iddef.
--iddef 0|1|2|3|4
Change the pairwise identity definition used in --id. Values accepted are:
0. CD-HIT definition: (matching columns) / (shortest sequence length).
1. edit distance: (matching columns) / (alignment length).
2. edit distance excluding terminal gaps (same as --id).
3. Marine Biological Lab definition counting each gap opening (internal or
terminal) as a single mismatch, whether or not the gap was extended: 1.0 -
[(mismatches + gap openings)/(longest sequence length)]
4. BLAST definition, equivalent to --iddef 1 in a context of global pairwise
alignment.
--lengthout
Write sequence length information to the output files in FASTA format by adding a
";length=integer" attribute in the header.
--minsize positive integer
Specify the minimum abundance of sequences for denoising using --cluster_unoise. The
default is 8.
--msaout filename
Output a multiple sequence alignment and a consensus sequence for each cluster to
filename, in fasta format. Be warned that vsearch computes center star multiple sequence
alignments using a fast method whose accuracy can decrease significantly when using low
pairwise identity thresholds. The consensus sequence is constructed by taking the
majority symbol (nucleotide or gap) from each column of the alignment. Columns containing
a majority of gaps are skipped, except for terminal gaps. If the --sizein option is
specified, sequence abundances will be taken into account when computing the consensus.
--mothur_shared_out filename
Output an OTU table in the mothur 'shared' tab-separated plain text format as described
at (link) ⟨https://www.mothur.org/wiki/Shared_file⟩
<https://www.mothur.org/wiki/Shared_file>. The format describes how a matrix containing
the abundances of the OTUs in the different samples is stored. The first line will start
with the strings 'label', 'group' and 'numOtus' and is followed by a list of all OTU
identifiers. The following lines, one for each sample, starts with the string 'vsearch'
followed by the sample identifier, the total number of OTUs, and a list of abundances for
each OTU in that sample, in the order given on the first line. The OTU and sample
identifiers are extracted from the FASTA headers of the sequences. The OTUs are
represented by the cluster centroids. See the --biomout option for further details.
--otutabout filename
Output an OTU table in the classic tab-separated plain text format as a matrix containing
the abundances of the OTUs in the different samples. The first line will start with the
string '#OTU ID' and is followed by a tab-separated list of all sample identifiers. The
following lines, one for each OTU, starts with the OTU identifier and is followed by a
tab-separated list of abundances for that OTU in each sample, in the order given on the
first line. The OTU and sample identifiers are extracted from the FASTA headers of the
sequences. The OTUs are represented by the cluster centroids. An extra column is added to
the right of the table if taxonomy information is available for at least one of the OTUs.
This column will be labelled 'taxonomy' and each row will then contain the taxonomy
information extracted for that OTU. See the --biomout option for further details.
--profile filename
Output a sequence profile to a text file with the frequency of each nucleotide in each
position in the multiple alignment for each cluster. There is a FASTA-like header line
for each cluster, followed by the profile information in a tab-separated format. The
eight columns are: position (0-based), consensus nucleotide, number of As, number of Cs,
number of Gs, number of Ts or Us, number of gap symbols, and finally the total number of
ambiguous nucleotide symbols (B, D, H, K, M, N, R, S, Y, V or W). All numbers are
integers. If the --sizein option is specified, sequence abundances will be taken into
account.
--qmask none|dust|soft
Mask regions in sequences using the dust or the soft methods, or do not mask (none).
Warning, when using soft masking, clustering becomes case sensitive. The default is to
mask using dust.
--qsegout filename
Write the aligned part of each query sequence to filename in FASTA format.
--relabel string
Relabel sequence identifiers in the output files produced by --consout, --profile and
--centroids options. Please see the description of the same option under Chimera
detection for details.
--relabel_keep
When relabelling, keep the old identifier in the header after a space.
--relabel_md5
Relabel sequence identifiers in the output files produced by --consout, --profile and
--centroids options. Please see the description of the same option under Chimera
detection for details.
--relabel_self
Relabel sequence identifiers in the output files produced by --consout, --profile and
--centroids options. Please see the description of the same option under Chimera
detection for details.
--relabel_sha1
Relabel sequence identifiers in the output files produced by --consout, --profile and
--centroids options. Please see the description of the same option under Chimera
detection for details.
--sizein Take into account the abundance annotations present in the input fasta file (search for
the pattern '[>;]size=integer[;]' in sequence headers).
--sizeorder
When an amplicon is close to 2 or more centroids, both within the distance specified with
the --id option, resolve the ambiguity by clustering it with the centroid having the
highest abundance, not necessarily the closest one. The option only has effect when the
value specified with --maxaccepts is higher than one. The --sizeorder option turns on
what is sometimes referred to as abundance-based greedy clustering (AGC), in contrast to
the default distance-based greedy clustering (DGC).
--sizeout
Add abundance annotations to the output fasta files (add the pattern ';size=integer;' to
sequence headers). If --sizein is specified, abundance annotations are reported to output
files, and each cluster centroid receives a new abundance value corresponding to the
total abundance of the amplicons included in the cluster (--centroids option). If
--sizein is not specified, input abundances are set to 1 for amplicons, and to the number
of amplicons per cluster for centroids.
--strand plus|both
When comparing sequences with the cluster seed, check the plus strand only (default) or
check both strands.
--tsegout filename
Write the aligned part of each target sequence to filename in FASTA format.
--uc filename
Output clustering results in filename using a tab-separated uclust-like format with 10
columns and 3 different type of entries (S, H or C). Each fasta sequence in the input
file can be either a cluster centroid (S) or a hit (H) assigned to a cluster. Cluster
records (C) summarize information (size, centroid label) for each cluster. In the context
of clustering, the option --uc_allhits has no effect on the --uc output. Column content
varies with the type of entry (S, H or C):
1. Record type: S, H, or C.
2. Cluster number (zero-based).
3. Centroid length (S), query length (H), or cluster size (C).
4. Percentage of similarity with the centroid sequence (H), or set to '*' (S, C).
5. Match orientation + or - (H), or set to '*' (S, C).
6. Not used, always set to '*' (S, C) or to zero (H).
7. Not used, always set to '*' (S, C) or to zero (H).
8. set to '*' (S, C) or, for H, compact representation of the pairwise alignment
using the CIGAR format (Compact Idiosyncratic Gapped Alignment Report): M
(match/mismatch), D (deletion) and I (insertion). The equal sign '=' indicates
that the query is identical to the centroid sequence.
9. Label of the query sequence (H), or of the centroid sequence (S, C).
10. Label of the centroid sequence (H), or set to '*' (S, C).
--unoise_alpha real
Specify the alpha parameter to the --cluster_unoise command. The default is 2.0.
--usersort
When using --cluster_smallmem, allow any sequence input order, not just a decreasing
length ordering.
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
--xsize Strip abundance information from the headers when writing the output file.
... Most searching options as well as score filtering, gap penalties and masking also apply
to clustering (see the Searching section for definitions): --alnout, --blast6out,
--fastapairs, --matched, --notmatched, --maxaccept, --maxreject, --samout, --userout,
--userfields
Dereplication and rereplication options:
VSEARCH can dereplicate sequences with the commands --derep_fulllength, --derep_id,
--derep_smallmem, --derep_prefix and --fastx_uniques. The --derep_fulllength command is
depreciated and is replaced by the new --fastx_uniques command that can also handle FASTQ files in
addition to FASTA files. The --derep_fulllength, --derep_smallmem, and --fastx_uniques commands
requires strictly identical sequences of the same length, but ignores upper/lower case and treats
T and U as identical symbols. The --derep_id command requires both identical sequences and
identical headers/labels. The --derep_prefix command will group sequences with a common prefix and
does not require them to be equally long. The --derep_smallmem uses a much smaller amount of
memory when dereplicating than the other files, and may be a bit slower and cannot read the input
from a pipe. It takes both FASTA and FASTQ files as input but only writes FASTA output to the file
specified with the --fastaout option. The --fastx_uniques command can write FASTQ output
(specified with --fastqout) or FASTA output (specified with --fastaout) as well as a special tab-
separated column text format (with --tabbedout). The other commands can write FASTA output to the
file specified with the --output option. All dereplication commands, except --derep_smallmem, can
write output to a special UCLUST-like file specified with the --uc option. The --rereplicate
command can duplicate sequences in the input file according to the abundance of each input
sequence. Other valid options are --fastq_ascii, --fastq_asciiout, --fastq_qmax, --fastq_qmaxout,
--fastq_qmin, --fastq_qminout, --fastq_qout_max, --lengthout, --maxuniquesize, --minuniquesize,
--relabel, --relabel_keep, --relabel_md5, --relabel_self, --relabel_sha1, --sizein, --sizeout,
--strand, --topn, --xlength, and --xsize.
--derep_fulllength filename
Merge strictly identical sequences contained in filename. Identical sequences are defined
as having the same length and the same string of nucleotides (case insensitive, T and U
are considered the same). See the options --sizein and --sizeout to take into account and
compute abundance values. This command does not support multithreading.
--derep_id filename
Merge strictly identical sequences contained in filename, as with the --derep_fulllength
command, but the sequence labels (identifiers) on the header line need to be identical
too.
--derep_smallmem filename
Merge strictly identical sequences contained in filename, as with the --derep_fulllength
command, but using much less memory. The output is written to a FASTA file specified with
the --fastaout option. The output is written in the order that the sequences first appear
in the input, and not in descending abundance order as with the other dereplication
commands. It can read, but not write FASTQ files. This command cannot read from a pipe,
it must be a proper file, as it is read twice. Dereplication is performed with a 128 bit
hash function and it is not verified that grouped sequences are identical, however the
probability that two different sequences are grouped in a dataset of 1 000 000 000 unique
sequences is approximately 1e-21. Memory footprint is appr. 24 bytes times the number of
unique sequence. Multithreading and the options --topn, --uc, or --tabbedout are not
supported.
--derep_prefix filename
Merge sequences with identical prefixes contained in filename. A short sequence
identical to an initial segment (prefix) of another sequence is considered a replicate of
the longer sequence. If a sequence is identical to the prefix of two or more longer
sequences, it is clustered with the shortest of them. If they are equally long, it is
clustered with the most abundant. Remaining ties are solved using sequence headers and
sequence input order. Sequence comparisons are case insensitive, and T and U are
considered identical. This command does not support multithreading.
--fastaout filename
Write the dereplicated sequences to filename, in fasta format and sorted by decreasing
abundance. Identical sequences receive the header of the first sequence of their group.
If --sizeout is used, the number of occurrences (i.e. abundance) of each sequence is
indicated at the end of their fasta header using the pattern ';size=integer;'. This
option is only valid for --fastx_uniques and --derep_smallmem.
--fastqout filename
Write the dereplicated sequences to filename, in fastq format and sorted by decreasing
abundance. Identical sequences receive the header of the first sequence of their group.
If --sizeout is used, the number of occurrences (i.e. abundance) of each sequence is
indicated at the end of their fastq header using the pattern ';size=integer;'. This
option is only valid for --fastx_uniques.
--fastq_ascii positive integer
Define the ASCII character number used as the basis for the FASTQ quality score. The
default is 33, which is used by the Sanger / Illumina 1.8+ FASTQ format (phred+33). The
value 64 is used by the Solexa, Illumina 1.3+ and Illumina 1.5+ formats (phred+64). Only
33 and 64 are valid arguments.
--fastq_asciiout positive integer
When using --fastq_convert, --sff_convert or --fasta2fastq, define the ASCII character
number used as the basis for the FASTQ quality score when writing FASTQ output files. The
default is 33. Only 33 and 64 are valid arguments.
--fastq_qmax positive integer
Specify the maximum quality score accepted when reading FASTQ files. The default is 41,
which is usual for recent Sanger/Illumina 1.8+ files.
--fastq_qmaxout positive integer
Specify the maximum quality score used when writing FASTQ files. The default is 41, which
is usual for recent Sanger/Illumina 1.8+ files. Older formats may use a maximum quality
score of 40.
--fastq_qmin positive integer
Specify the minimum quality score accepted for FASTQ files. The default is 0, which is
usual for recent Sanger/Illumina 1.8+ files. Older formats may use scores between -5 and
2.
--fastq_qminout positive integer
Specify the minimum quality score used when writing FASTQ files. The default is 0, which
is usual for Sanger/Illumina 1.8+ files. Older versions of the format may use scores
between -5 and 2.
--fastq_qout_max
For --fastx_uniques, indicate that the new quality scores computed when dereplicating
FASTQ files should be equal to the maximum (best) of the input quality scores for each
position (corresponding to the lowest error probability). The default is to output a
quality score corresponding to the average of the error probabilities for each position.
--fastx_uniques filename
Merge strictly identical sequences contained in FASTA or FASTQ file filename. Identical
sequences are defined as having the same length and the same string of nucleotides (case
insensitive, T and U are considered the same). See the options --sizein and --sizeout to
take into account and compute abundance values. This command does not support
multithreading. By default, the quality scores in FASTQ output files will correspond to
the average error probability of the nucleotides in the each position. If the
--fastq_qout_max option is given, the quality score will be the highest (best) quality
score observed in each position.
--lengthout
Write sequence length information to the output files in FASTA and FASTQ format by adding
a ";length=integer" attribute in the header.
--maxuniquesize positive integer
Discard sequences with a post-dereplication abundance value greater than integer.
--minuniquesize positive integer
Discard sequences with a post-dereplication abundance value smaller than integer.
--output filename
Write the dereplicated sequences to filename, in fasta format and sorted by decreasing
abundance. Identical sequences receive the header of the first sequence of their group.
If --sizeout is used, the number of occurrences (i.e. abundance) of each sequence is
indicated at the end of their fasta header using the pattern ';size=integer;'. This
option is not allowed for --fastx_uniques or --derep_smallmem.
--relabel string
Please see the description of the same option under Chimera detection for details.
--relabel_keep
When relabelling, keep the old identifier in the header after a space.
--relabel_md5
Please see the description of the same option under Chimera detection for details.
--relabel_self
Please see the description of the same option under Chimera detection for details.
--relabel_sha1
Please see the description of the same option under Chimera detection for details.
--rereplicate filename
Duplicate each sequence the number of times indicated by the abundance of each sequence
in the specified file (option --sizein is always implied). The sequence labels are
identical for the same sequence, unless --relabel, --relabel_self, --relabel_sha1 or
--relabel_md5 is used to create unique labels. Output is written to the file specified
with the --output option, in FASTA format. The output file does not contain abundance
information unless --sizeout is specified, in which case an abundance of 1 is used.
--sizein Take into account the abundance annotations present in the input fasta file (search for
the pattern '[>;]size=integer[;]' in sequence headers). That option is active by default
when rereplicating.
--sizeout
Add abundance annotations to the output fasta file (add the pattern ';size=integer;' to
sequence headers). If --sizein is specified, each unique sequence receives a new
abundance value corresponding to its total abundance (sum of the abundances of its
occurrences). If --sizein is not specified, input abundances are set to 1, and each
unique sequence receives a new abundance value corresponding to its number of occurrences
in the input file.
--strand plus|both
When searching for strictly identical sequences, check the plus strand only (default) or
check both strands.
--tabbedout filename
Output clustering info to the specified tab-separated text file with 6 columns and a row
for each input sequence. Column 1 contains the original label/header of the sequence.
Column 2 contains the label of the output sequence which is equal to the label/header of
the first sequence in each cluster, but potentially relabelled. Column 3 contains the
cluster number, starting from 0. Column 4 contains the sequence number within each
cluster, starting at 0. Column 5 contains the number of sequences in the cluster. Column
6 contains the original label/header of the first sequence in the cluster before any
potential relabelling. This option is only valid for the --fastx_uniques command.
--topn positive integer
Output only the top integer sequences (i.e. the most abundant).
--uc filename
Output full-length or prefix-dereplication results in filename using a tab-separated
uclust-like format with 10 columns and 3 different type of entries (S, H or C). Each
fasta sequence in the input file can be either a cluster centroid (S) or a hit (H)
assigned to a cluster. Cluster records (C) summarize information (size, centroid label)
for each cluster. In the context of dereplication, the option --uc_allhits has no effect
on the --uc output. Column content varies with the type of entry (S, H or C):
1. Record type: S, H, or C.
2. Cluster number (zero-based).
3. Sequence length (S, H), or cluster size (C).
4. Percentage of similarity with the centroid sequence (H), or set to '*' (S, C).
5. Match orientation + or - (H), or set to '*' (S, C).
6. Not used, always set to '*' (S, C) or 0 (H).
7. Not used, always set to '*' (S, C) or 0 (H).
8. Not used, always set to '*'.
9. Label of the query sequence (H), or of the centroid sequence (S, C).
10. Label of the centroid sequence (H), or set to '*' (S, C).
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
--xsize
Strip abundance information from the headers when writing the output file.
Extraction options:
Sequences with headers matching certain criteria can be extracted from FASTA and FASTQ files using
the --fastx_getseq, --fastx_getseqs and --fastx_getsubseq commands.
The --fastx_getseq command requires the header to match a label specified with the --label option.
If the --label_substr_match option is given, the label may be a substring located anywhere in the
header, otherwise the entire header must match the label. These matches are not case-sensitive.
The headers in the input file are truncated at the first space or tab character unless the
--notrunclabels option is given. The matching sequences will be written to the files specified
with the --fastaout and --fastqout options, in FASTA and FASTQ format, respectively. Sequences
that do not match are written to the files specified with the --notmatched and --notmatchedfq
options, respectively.
The --fastx_getsubseq command is similar to the --fastx_getseq command, but will extract a
subsequence of the matching sequences. The start position is specified with the --subseq_start
option and the end position is specified with the --subseq_end option. The positions are 1-based,
meaning that the first symbol of the sequence is at position 1. If the start or end position
option is not specified, the default is to start at the first position and end at the last
position in the sequence.
The --fastx_getseqs command is similar to the --fastx_getseq command but allows more flexibility
in specifying the label(s) to be matched. A single label may be specified using the --label option
as described above. Alternatively, a file containing a list of labels to be matched may be
specified with the --labels option. The file must be a plain text file with one label on each
line. The --label_word and --label_words options may be used to specify either a single word or a
file containing a list of words, respectively, to be matched. Words are defined as character
sequences delimited either by a character that is not alpha-numeric (A-Z, a-z, or 0-9) or by the
beginning or end of the header. Word matching is case-sensitive. The --label_field option will
limit the matching of words to a certain field in the header.
--fastaout filename
Write the extracted sequences in FASTA format to the file with the given name.
--fastqout filename
Write the extracted sequences in FASTQ format to the file with the given name. This
option is illegal if the input is in FASTA format.
--fastx_getseq filename
Extract sequences from the given FASTA or FASTQ file. Specify a label to match using the
--label option. Output files are specified with the --fastaout, --fastqout, --notmatched
and --notmatchedfq options.
--fastx_getseqs filename
Extract sequences from the given FASTA or FASTQ file. Specify the label or labels to
match using one of the following options: --label, --labels, --label_word, or
--label_words. Output files are specified with the --fastaout, --fastqout, --notmatched
and --notmatchedfq options.
--fastx_getsubseq filename
Extract a certain part of some of the sequences in the given FASTA or FASTQ file. Specify
labels to match using the --label option. Specify the subsequence range to be extracted
with the --subseq_start and --subseq_end options. Output files are specified with the
--fastaout, --fastqout, --notmatched and --notmatchedfq options.
--label string
Specify the label to match in the sequence header. Unless the --label_substr_match option
is given, the label must match the entire header. The comparison is not case-sensitive.
--label_field string
Specify a field name to be used when matching using the --label_word or --label_words
option. The field name is a string like "abc" that must precede the word to be matched
with an equals sign (=) in between. The field must be delimited by semicolons or the
beginning or end of the header. The following header will match the label 123 in the
field abc: "seq1;abc=123".
--label_substr_match
The labels specified with the --label or the --labels option may match anywhere in the
header if this option is given. Otherwise a label needs to match the entire header.
--label_word string
Specify a word to match in the sequence header. Words are defined as strings delimited by
either the start or end of the header or by any symbol that is not a letter (A-Z, a-z) or
digit (0-9). The comparison is case-sensitive.
--label_words filename
Specify a file containing words to be matched against the sequence headers. The plain
text file must contain one word on each line. Words are defined as strings delimited by
either the start or end of the header or by any symbol that is not a letter (A-Z, a-z) or
digit (0-9). The comparison is case-sensitive.
--labels filename
Specify a file containing labels to be matched against the sequence headers. The plain
text file must contain one label on each line. Unless the --label_substr_match option is
given, a label must match the entire header. The comparison is not case-sensitive.
--notmatched filename
Write the sequences that were not extracted to the file with the given name, in FASTA
format.
--notmatchedfq filename
Write the sequences that were not extracted to the file with the given name, in FASTQ
format. This option is illegal if the input is in FASTA format.
--subseq_end positive integer
Specify the end position in the sequences when extracting subsequences using the
--fastx_getsubseq command. Positions are 1-based, so the sequences start at position 1.
The default is to end at the end of the sequence if this option is not specified.
--subseq_start positive integer
Specify the starting position in the sequences when extracting subsequences using the
--fastx_getsubseq command. Positions are 1-based, so the sequences start at position 1.
The default is to start at the beginning of the sequence (position 1), if this option is
not specified.
FASTA/FASTQ/SFF file processing options:
Analyse, trim, filter, convert, merge, join or reverse complement sequences in FASTA, FASTQ or SFF
files. The --fastq_chars command can be used to analyse FASTQ files to identify the quality
encoding and the range of quality score values used. To convert between different FASTQ file
variants, use the --fastq_convert command. Statistical analysis of the quality and length of the
sequences in a FASTQ file may be performed with the --fastq_stats, --fastq_eestats, and
--fastq_eestats2 commands. Sequences may be trimmed, filtered and converted by the --fastq_filter
or --fastx_filter commands. The --sff_convert command can be used to convert SFF files to FASTQ,
while the --fasta2fastq command will convert a FASTA file to a FASTQ file with fake quality
scores. Paired-end reads can be merged using the --fastq_mergepairs command or joined with the
--fastq_join command. The --fastx_revcomp command will reverse-complements sequences.
--eeout When using --fastq_filter, --fastx_filter or --fastq_mergepairs, include the number of
expected errors (ee) in the sequence header of FASTQ and FASTA output files. This option
is a synonym of the --fastq_eeout option. Use the --xee option to remove this information
from headers.
--eetabbedout filename
When specified with the --fastq_mergepairs command, write statistics with expected errors
of each merged read to the given file. The file is a tab separated file with four
columns: The number of expected errors in the forward read, the number of expected errors
in the reverse read, the number of observed errors in the forward read, and the number of
observed errors in the reverse read. The observed number of errors are the number of
differences in the overlap region of the merged sequence relative to each of the reads in
the pair.
--fasta2fastq filename
Add a fake nucleotide quality score to the sequences in the given FASTA file and write
them to the FASTQ file specified with the --fastqout option. The quality score may be
adjusted using the --fastq_qmaxout option (default 41). The --fastq_asciiout option may
be used to adjust the FASTQ output quality ASCII base character (default 33).
--fastaout filename
When using --fastq_filter, --fastq_mergepairs or --fastx_filter, write to the given
FASTA-formatted file the sequences passing the filter, or the merged sequences.
--fastaout_rev filename
When using --fastq_filter, or --fastx_filter, write to the given FASTA-formatted file the
reverse reads passing the filter.
--fastaout_notmerged_fwd filename
When using --fastq_mergepairs, write forward reads not merged to the specified FASTA
file.
--fastaout_notmerged_rev filename
When using --fastq_mergepairs, write reverse reads not merged to the specified FASTA
file.
--fastaout_discarded filename
Write sequences that do not pass the filter of the --fastq_filter or --fastx_filter
command to the given FASTA-formatted file.
--fastaout_discarded_rev filename
Write reverse reads that do not pass the filter of the --fastq_filter or --fastx_filter
command to the given FASTA-formatted file.
--fastq_allowmergestagger
When using --fastq_mergepairs, allow merging of staggered read pairs. Staggered pairs are
pairs where the 3' end of the reverse read has an overhang to the left of the 5' end of
the forward read. This situation can occur when a very short fragment is sequenced. The
3' overhang of the reverse read is not included in the merged sequence. The opposite
option is the --fastq_nostagger option. The default is to discard staggered pairs.
--fastq_ascii positive integer
Define the ASCII character number used as the basis for the FASTQ quality score. The
default is 33, which is used by the Sanger / Illumina 1.8+ FASTQ format (phred+33). The
value 64 is used by the Solexa, Illumina 1.3+ and Illumina 1.5+ formats (phred+64). Only
33 and 64 are valid arguments.
--fastq_asciiout positive integer
When using --fastq_convert, --sff_convert or --fasta2fastq, define the ASCII character
number used as the basis for the FASTQ quality score when writing FASTQ output files. The
default is 33. Only 33 and 64 are valid arguments.
--fastq_chars filename
Summarize the composition of sequence and quality strings contained in the input FASTQ
file. For each of the four DNA letters, --fastq_chars gives the number of occurrences of
the letter, its relative frequency and the length of the longest run of that letter. For
each character present in the quality strings, --fastq_chars gives the ASCII value of the
character, its relative frequency, and the number of times a k-mer of that character
appears at the end of quality strings. The length of the k-mer can be set using
--fastq_tail (4 by default). The command --fastq_chars tries to automatically detect the
quality encoding (Solexa, Illumina 1.3+, Illumina 1.5+ or Illumina 1.8+/Sanger) by
analyzing the range of observed quality score values. In case of success, --fastq_chars
suggests values for the --fastq_ascii (33 or 64), --fastq_qmin and --fastq_qmax options
to be used with the other commands that require a FASTQ input file.
--fastq_convert filename
Convert between the different variants of the FASTQ file format. The quality encoding of
the input file must be specified with the --fastq_ascii option (either 33 or 64, the
default is 33), and the output quality encoding must be specified with the
--fastq_asciiout option (default 33). The minimum and maximum output quality scores may
be limited using the --fastq_qminout and --fastq_qmaxout options. The output file is
specified with the --fastqout option.
--fastq_eeout
When using --fastq_filter, --fastx_filter or --fastq_mergepairs, include the number of
expected errors (ee) in the sequence header of FASTQ and FASTA files. This option is a
synonym of the --eeout option. Use the --xee option to remove this information from
headers.
--fastq_eestats filename
Analyze a FASTQ file and report statistics on the distributions of quality scores, error
probabilities and expected accumulated errors. The report, a table of 21 tab-separated
columns, is written to the file specified with the --output option. The first column
corresponds to the position in the reads (Pos). The second and third columns correspond
to the number of reads (Reads) and percentage of reads (PctRecs) that include this
position. The remaining columns include information about the distribution of quality
scores in this position (Q), error probabilities in this position (Pe), and finally the
expected number of accumulated errors from the beginning of the reads and until the
current position (EE). For each of the Q, Pe and EE distributions, the following
statistics are included: minimum value (Min), lower quartile (Low), median (Med), mean
(Mean), upper quartile (Hi), and maximum value (Max). The quality encoding and the range
of quality values may be specified with --fastq_ascii --fastq_qmin and --fastq_qmax.
--fastq_eestats2 filename
Analyze the specified FASTQ file and report statistics on the number of sequences that
would be retained at a combination of selected cutoffs for length truncation and maximum
expected errors, that could potentially be used as arguments to the --fastq_trunclen and
--fastq_maxee options to the --fastq_filter command. The result, a table of two or more
columns, is written to the file specified with the --output option. There is a line for
each length truncation cutoff. The first column on each line contains the selected
truncation length, while the following columns contain the number of sequences and, in
parenthesis, the percentage of sequences that would be retained at the selected EE
levels. The truncation length cutoffs may be specified with the --length_cutoffs option
and requires a list of three comma-separated integers indicating the shortest cutoff, the
longest cutoff, and the increment between cutoffs. The longest cutoff may be specified
with a star (*) which indicates that the limit is equal to the longest sequence in the
input file. The default setting is "50,*,50" meaning that truncation lengths of 50, 100,
150 and so on up to the longest sequence length should be used. The maximum expected
error (EE) cutoffs may be specified with the --ee_cutoffs option which requires a comma-
separated list of floating point numbers as its argument. The default setting is
"0.5,1.0,2.0" that indicates that expected error levels of 0.5, 1.0 and 2.0 should be
used.
--fastq_filter filename
Trim and/or filter sequences in the given FASTQ file. Similar to the --fastx_filter
command, but works only on FASTQ files. See --fastx_filter for details.
--fastq_join filename
Join paired-end sequence reads into one sequence and add a gap between them using a
padding sequence. The sequences are not merged as with the fastq_mergepairs command, but
simply joined with a gap. The forward reads are specified as the argument to this option
and the reverse reads are specified with the --reverse option. The resulting sequences
consist of the forward read, the padding sequence and the reverse complement of the
reverse read. The padding sequence is specified with the --join_padgap option and the
padding quality is specified with the --join_padgapq option. The default padding sequence
string is NNNNNNNN and the default padding quality string is IIIIIIII, corresponding to a
base quality score of 40 (a very high quality score with error probability 0.0001). The
joined sequences are output to the file(s) specified with the --fastaout or --fastqout
options.
--fastq_maxdiffs positive integer
When using --fastq_mergepairs, specify the maximum number of non-matching nucleotides
allowed in the overlap region. That option has a strong influence on the merging success
rate. The default value is 10.
--fastq_maxdiffpct real
When using --fastq_mergepairs, specify the maximum percentage of non-matching nucleotides
allowed in the overlap region. The default value is 100.0%. There are other more
sophisticated rules in the merging algorithm that will discard read pairs with a high
fraction of mismatches.
--fastq_maxee real
When using --fastq_filter, --fastq_mergepairs or --fastx_filter, discard sequences with
an expected error greater than the specified number (value ranging from 0.0 to infinity).
For a given sequence, the expected error is the sum of error probabilities for all the
positions in the sequence. Since error probabilities can be small but not null, the
expected error is always greater than zero, and at most equal to the length of the
sequence when all positions in the sequence have an error probability of 1.0.
Using the expected error as the lambda parameter in the Poisson distribution, it is
possible to compute the probability of observing k errors. For instance, a read with an
expected error of 1.0 has:
- 36.8% chance of having zero error,
- 36.8% chance of having one error,
- 18.4% chance of having two errors,
- 6.1% chance of having three errors,
- 1.5% chance of having four errors,
- 0.3% chance of having five errors,
- etc.
--fastq_maxee_rate real
When using --fastq_filter or --fastx_filter, discard sequences with an average expected
error greater than the specified number (value ranging from 0.0 to 1.0 included). For a
given sequence, the average expected error is the sum of error probabilities for all the
positions in the sequence, divided by the length of the sequence.
--fastq_maxlen positive integer
When using --fastq_filter, --fastq_mergepairs or --fastx_filter, discard sequences with
more than the specified number of bases.
--fastq_maxmergelen positive integer
When using --fastq_mergepairs, specify the maximum length of the merged sequence (default
is 1,000,000).
--fastq_maxns positive integer
When using --fastq_filter, --fastq_mergepairs or --fastx_filter, discard sequences with
more than the specified number of N's.
--fastq_mergepairs filename
Merge paired-end sequence reads into one sequence. The forward reads are specified as the
argument to this option and the reverse reads are specified with the --reverse option.
Reads with the same index/position in the forward and reverse files are considered to form
a pair, even if their labels are different. Thus, forward and reverse reads must appear in
the same order and total number in both files. A warning is emitted if the forward and
reverse files contain different numbers of reads. The merged sequences are written to the
file(s) specified with the --fastaout or --fastqout options. The non-merged reads can be
output to the files specified with the --fastaout_notmerged_fwd, --fastaout_notmerged_rev,
--fastqout_notmerged_fwd and --fastqout_notmerged_rev options. Statistics may be output to
the file specified with the --eetabbedout option. Sequences are truncated as specified with
the --fastq_truncqual option to remove low-quality bases in the 3' end. Sequences shorter
than specified with --fastq_minlen (after truncation) are discarded (1 by default).
Sequences with too many ambiguous bases (N's), as specified with the --fastq_maxns are also
discarded (no limit by default). Staggered reads are not merged unless the
--fastq_allowmergestagger option is specified. The minimum length of the overlap region
between the reads may be specified with the --fastq_minovlen option (at least 5, default
10). The overlap region may not include more mismatches than specified with the
--fastq_maxdiffs option (10 by default) or a higher percentage of mismatches than specified
with the --fastq_maxdiffpct option (100.0% by default), otherwise the read pair is
discarded. Additional rules will avoid merging of reads that cannot be aligned reliably and
unambiguously. The minimum and maximum length of the merged sequence may be specified with
the --fastq_minmergelen and --fastq_maxmergelen options, respectively. The quality value
limits for output files may be specified with the --fastq_qminout and --fastq_qmaxout
options, but they apply only to the merged region. Other relevant options are:
--fastq_ascii, --fastq_maxee, --fastq_nostagger, --fastq_qmax, --fastq_qmin, and
--label_suffix.
--fastq_minlen positive integer
When using --fastq_filter, --fastq_mergepairs or --fastx_filter, discard input sequences
with less than the specified number of bases (default 1).
--fastq_minmergelen positive integer
When using --fastq_mergepairs, specify the minimum length of the merged sequence. The
default is 1.
--fastq_minovlen positive integer
When using --fastq_mergepairs, specify the minimum overlap between the merged reads. The
default is 10. Must be at least 5.
--fastq_nostagger
When using --fastq_mergepairs, forbid the merging of staggered read pairs. This is the
default behaviour of --fastq_mergepairs. To change that behaviour, see the
--fastq_allowmergestagger option.
--fastq_qmax positive integer
Specify the maximum quality score accepted when reading FASTQ files. The default is 41,
which is usual for recent Sanger/Illumina 1.8+ files.
--fastq_qmaxout positive integer
When using --fastq_mergepairs, --fastq_convert, --sff_convert or --fasta2fastq, specify the
maximum quality score used when writing FASTQ files. For the --fasta2fastq command, the
value specified here is the fake quality score used for the FASTQ output file. The default
is 41, which is usual for recent Sanger/Illumina 1.8+ files. Older formats may use a
maximum quality score of 40. The limit only applies to the merged region when using
--fastq_mergepairs.
--fastq_qmin positive integer
Specify the minimum quality score accepted for FASTQ files. The default is 0, which is
usual for recent Sanger/Illumina 1.8+ files. Older formats may use scores between -5 and 2.
--fastq_qminout positive integer
When using --fastq_mergepairs, --fastq_convert or --sff_convert, specify the minimum
quality score used when writing FASTQ files. The default is 0, which is usual for
Sanger/Illumina 1.8+ files. Older versions of the format may use scores between -5 and 2.
The limit applies only to the merged region when using --fastq_mergepairs.
--fastq_stats filename
Analyze a FASTQ file and report the number of reads it contains. The quality encoding and
the range of quality values may be specified with --fastq_ascii --fastq_qmin and
--fastq_qmax. That command requires the --log option and outputs the following detailed
statistics on read length, quality score, length vs. quality distributions, and length /
quality filtering:
Read length distribution:
1. L: read length.
2. N: number of reads.
3. Pct: fraction of reads with this length.
4: AccPct: fraction of reads with this length or longer.
Quality score distribution:
1. ASCII: character encoding the quality score.
2. Q: Phred quality score.
3. Pe: probability of error associated with the quality score.
4. N: number of bases with this quality score.
5. Pct: fraction of bases with this quality score.
6: AccPct: fraction of bases with this quality score or higher.
Length vs. quality distribution:
1. L: position in reads (starting from position 2).
2. PctRecs: fraction of reads with at least this length.
3. AvgQ: average quality score over all reads up to this position.
4. P(AvgQ): error probability corresponding to AvgQ.
5. AvgP: average error probability.
6: AvgEE: average expected error over all reads up to this position.
7: Rate: growth rate of AvgEE between this position and position - 1.
8: RatePct: Rate (as explained above) expressed as a percentage.
Effect of expected error and length filtering:
The first column indicates read lengths (L). The next four columns indicate the
number of reads that would be retained by the --fastq_filter command if the reads
were truncated at length L (option --fastq_trunclen L) and filtered to have a
maximum expected error of 1.0, 0.5, 0.25 or 0.1 (with the option --fastq_maxee
float). The last four columns indicate the fraction of reads that would be retained
by the --fastq_filter command using the same length and maximum expected error
parameters.
Effect of minimum quality and length filtering:
The first column indicates read lengths (Len). The next four columns indicate the
fraction of reads that would be retained by the --fastq_filter command if the reads
were truncated at length Len (option --fastq_trunclen Len) or at the first position
with a quality Q below 5, 10, 15 or 20 (option --fastq_truncqual Q).
--fastq_stripleft positive integer
When using --fastq_filter or --fastx_filter, strip the specified number of bases from the
left end of the reads. If the length of the resulting read is null, then the read is
discarded.
--fastq_stripright positive integer
When using --fastq_filter or --fastx_filter, strip the specified number of bases from the
right end of the reads. If the length of the resulting read is null, then the read is
discarded.
--fastq_tail positive integer
When using --fastq_chars, count the number of times a series of characters of length k
appears at the end of quality strings. By default, k = 4.
--fastq_truncee real
When using --fastq_filter or --fastx_filter, truncate sequences so that their total
expected error is not higher than the specified value.
--fastq_trunclen positive integer
When using --fastq_filter or --fastx_filter, truncate sequences to the specified length.
Shorter sequences are discarded.
--fastq_trunclen_keep positive integer
When using --fastq_filter or --fastx_filter, truncate sequences to the specified length.
Shorter sequences are not discarded.
--fastq_truncqual positive integer
When using --fastq_filter, --fastq_mergepairs or --fastx_filter, truncate sequences
starting from the first base with the specified base quality score value or lower.
--fastqout filename
When using --fastq_filter, --fastq_mergepairs, --fastx_filter or --fasta2fastq, write to
the given FASTQ-formatted file the sequences passing the filter, or the merged or converted
sequences.
--fastqout_rev filename
When using --fastq_filter or --fastx_filter, write to the given FASTQ-formatted file the
reverse reads passing the filter.
--fastqout_discarded filename
When using --fastq_filter or --fastx_filter, write sequences that do not pass the filter to
the given FASTQ-formatted file.
--fastqout_discarded_rev filename
When using --fastq_filter or --fastx_filter, write reverse reads that do not pass the
filter to the given FASTQ-formatted file.
--fastqout_notmerged_fwd filename
When using --fastq_mergepairs, write forward reads not merged to the specified FASTQ file.
--fastqout_notmerged_rev filename
When using --fastq_mergepairs, write reverse reads not merged to the specified FASTQ file.
--fastx_filter filename
Trim and/or filter the sequences in the given FASTA or FASTQ file and output the remaining
sequences to the FASTQ file specified with the --fastqout option and/or to the FASTA file
specified with the --fastaout option. Discarded sequences are written to the files
specified with the --fastaout_discarded and --fastqout_discarded options. The input format
(FASTA or FASTQ) is automatically detected. If the input consists of paired sequences, an
input file with reverse reads may be specified with the --reverse option, and corresponding
output will be written to the files specified with the --fastqout_rev, --fastaout_rev,
--fastqout_discarded_rev, and --fastaout_discarded_rev options. Output can not be written
to FASTQ files if the input is in FASTA format. The sequences are first trimmed and then
filtered based on the remaining bases. Sequences may be trimmed using the options
--fastq_stripleft, --fastq_stripright, --fastq_truncee, --fastq_trunclen,
--fastq_trunclen_keep and --fastq_truncqual. The sequences may be filtered using the
options --fastq_maxee, --fastq_maxee_rate, --fastq_maxlen, --fastq_maxns, --fastq_minlen
(default 1), --fastq_trunclen, --maxsize, and --minsize. Sequences not satisfying the
requirements are discarded. For pairs of sequences, both sequences in a pair must satisfy
the requirements, otherwise both are discarded. If no shortening or filtering options are
given, all sequences are written to the output files, possibly after conversion from FASTQ
to FASTA format. The --relabel option may be used to relabel the output sequences. The
--eeout option may be used to output the expected number of errors in each sequence. After
all sequences have been processed, the number of kept and discarded sequences will be
shown, as well as how many of the kept sequences were trimmed. When the input is in FASTA
format, the following options are not accepted because quality scores are not available:
--eeout, --fastq_ascii, --fastq_eeout, --fastq_maxee, --fastq_maxee_rate, --fastq_out,
--fastq_qmax, --fastq_qmin, --fastq_truncee, --fastq_truncqual, --fastqout_discarded,
--fastqout_discarded_rev, --fastqout_rev.
--fastx_revcomp filename
Reverse-complement the sequences in the given FASTA or FASTQ file to a file specified with
the --fastaout and/or --fastqout options. If the input file is in FASTA format, the output
can not be written back to a FASTQ file due to missing base quality scores.
--join_padgap string
When running --fastq_join, use the string as a sequence padding string. The default is
NNNNNNNN (8 N's).
--join_padgapq string
When running --fastq_join, use the string as a quality padding string. The default is a
string of I's equal in length to the sequence padding string. The letter I corresponds to a
base quality score of 40 indicating a very high quality base with error probability of
0.0001.
--lengthout
Write sequence length information to the output files in FASTA or FASTQ format by adding a
";length=integer" attribute in the header.
--maxsize positive integer
When using --fastq_filter or --fastx_filter, discard sequences with an abundance higher
than the specified value.
--minsize positive integer
When using --fastq_filter or --fastx_filter, discard sequences with an abundance lower than
the specified value.
--output filename
When using --fastq_eestats or --fastq_eestats2, write tabulated results to filename. See
--fastq_eestats's and --fastq_eestats2's documentation for a complete description of the
table.
--relabel_keep
When using --relabel, keep the old identifier in the header after a space.
--relabel string
Please see the description of the same option under Chimera detection for details.
--relabel_md5
Please see the description of the same option under Chimera detection for details.
--relabel_self
Please see the description of the same option under Chimera detection for details.
--relabel_sha1
Please see the description of the same option under Chimera detection for details.
--reverse filename
When using --fastq_filter, --fastx_filter, --fastq_mergepairs or --fastq_join, specify the
FASTQ file containing containing the reverse reads.
--sff_convert filename
Convert the given SFF file to FASTQ. The FASTQ output file is specified with the --fastqout
option. The sequence may be clipped as specified in the SFF file if the option --sff_clip
is specified, otherwise no clipping occurs. Bases that would have been clipped are
converted to lower case, while the rest is in upper case. The output quality encoding may
be specified with the --fastq_asciiout option (default 33). The minimum and maximum output
quality scores may be limited using the --fastq_qminout and --fastq_qmaxout options.
--sff_clip
Specifies that the sequences converted by the --sff_convert command should be clipped in
both ends as indicated in the SFF file. By default no clipping is performed.
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
--xsize
Strip abundance information from the headers when writing the output file.
--xee Strip information about expected errors (ee) from the output file headers. This information
is added by the --fastq_eeout and --eeout options.
Masking options:
An input sequence can be composed of lower- or uppercase letters. When soft masking is specified,
lower case letters are treated as symbols that should be masked. Otherwise the case of the input
sequences is ignored.
Masking is performed by the commands for chimera detection (uchime_denovo, uchime_ref), clustering
(cluster_fast, cluster_smallmem, cluster_size), masking (maskfasta, fastx_mask), pairwise
alignment (allpairs_global) and searching (search_exact, usearch_global).
Masking is usually specified with the --qmask option, while the --dbmask option is used for the
database sequences specified with the --db option with the --usearch_global, --search_exact and
--uchime_ref commands.
The argument to the --qmask and --dbmask option may be none, soft or dust. If the argument is
none, the no masking is performed. If the argument is soft the lower case symbols are masked.
Finally, if the argument is dust, the sequence is masked using the DUST algorithm by Tatusov and
Lipman to mask low-complexity regions.
If the --hardmask option is specified, all masked regions are converted to N's, otherwise masked
regions are indicated by lower case letters.
If any sequence is masked, the masked version of the sequence (with lower case letters or N's) is
used in all output files. Otherwise the sequence is unmodified. The exception is the sequences in
the output file specified with the --uchimealns option, where the input sequences are converted to
upper case first and lower case letters indicate disagreement between the aligned sequences.
The --qmask option (or --dbmask for database sequences) may be combined with the --hardmask
option. The results of using the none, dust or soft argument to --qmask or --dbmask are presented
below, assuming each input sequence contains both lower and uppercase symbols.
Results if the --hardmask option is off (default):
none: no masking, all symbols used, no change
dust: masked symbols lowercased, rest uppercased
soft: lowercase symbols masked, no case changes
Results if the --hardmask option is on:
none: no masking, all symbols used, no change
dust: masked symbols changed to Ns, rest unchanged
soft: lowercase symbols masked and changed to Ns
When a sequence region is masked, words in the region are not included in the indices used in the
heuristic search algorithm. In all other aspects, the region is treated as other regions.
Regions in sequences that are hardmasked (with N's) have a zero alignment score and do not
contribute to an alignment.
--fastaout filename
Write the masked sequences to filename, in fasta format. Applies only to the --fastx_mask
command.
--fastqout filename
Write the masked sequences to filename, in fastq format. Applies only to the --fastx_mask
command.
--fastx_mask filename
Mask regions in sequences contained in the specified fasta or fastq file. The default is
to mask using DUST (use --qmask to modify that behaviour). The output files are specified
with the --fastaout and --fastqout options. The minimum and maximum percentage of
unmasked residues may be specified with the --min_unmasked_pct and --max_unmasked_pct
options, respectively.
--hardmask
Symbols in masked regions are replaced by N's. The default is to replace the masked
regions by lower case letters.
--maskfasta filename
Mask regions in sequences contained in the fasta file filename. The default is to mask
using dust (use --qmask to modify that behaviour). The output file is specified with the
--output option. This command is depreciated, please use --fastx_mask instead.
--max_unmasked_pct real
Discard sequences with more than the specified maximum percentage of unmasked residues.
Works only with --fastx_mask.
--min_unmasked_pct real
Discard sequences with less than the specified minimum percentage of unmasked residues.
Works only with --fastx_mask.
--output filename
Write the masked sequences to filename, in fasta format. Applies only to the --mask_fasta
command.
--qmask none|dust|soft
If the argument is dust, mask regions in sequences using the DUST algorithm that detects
simple repeats and low-complexity regions. This is the default. If the argument is soft,
mask the lower case letters in the input sequence. If the argument is none, do not mask.
Orienting options:
The --orient command can be used to orient the sequences in a given file in either the forward or
the reverse complementary direction based on a reference database specified with the --db option.
The two strands of each input sequence are compared to the reference database using nucleotide
words. If one of the strands shares many more words with at least one sequence in the database
than the other, that strand is chosen. The correctly oriented sequences may be written to a FASTA
file specified with the --fastaout, and to a FASTQ file specified with the --fastqout option (as
long as the input was also in FASTQ format). If the result is uncertain, because the number of
matching words is too similar, the original sequence is written to the file specified with the
--notmatched option. The results may also be written to a tab-delimited text file specified with
the --tabbedout option. This file will contain the query label, the direction (+, - or ?), the
number of matching words on the forward strand, and the number of matching words on the reverse
complementary strand. By default, a word length of 12 is used for this command. The word length
may be adjusted using the --wordlength option. There has to be at least 4 times as many matches on
one strand than the other for a strand to be selected. In addition to the common options, the
following options may also be specified for this command: --dbmask, --qmask, --relabel,
--relabel_keep, --relabel_md5, --relabel_self, --relabel_sha1, --sizein, and --sizeout.
--db filename
Read the reference database from the given file. It may be in FASTA, FASTQ or UDB format.
If an UDB file is used it should have been created with a wordlength of 12.
--fastaout filename
Write the correctly oriented sequences to filename, in fasta format.
--fastqout filename
Write the correctly oriented sequences to filename, in fastq format.
--notmatched filename
Write the sequences with undetermined direction to filename, in the original format.
--orient filename
Orient the sequences in the given file.
--tabbedout filename
Write the resuls to a tab-delimited text file with the specified filename. This file will
contain the query label, the direction (+, - or ?), the number of matching words on the
forward strand, and the number of matching words on the reverse complementary strand.
Pairwise alignment options:
The results of the n * (n-1) / 2 pairwise alignments are written to the result files specified
with --alnout, --blast6out, --fastapairs --matched, --notmatched, --qsegout, --samout, --tsegout,
--uc or --userout (see Searching section below). Specify either the --acceptall option to output
all pairwise alignments, or specify an identity level with --id to discard weak alignments. Most
other accept/reject options (see Searching options below) may also be used. Sequences are aligned
on their plus strand only. Masking is performed as usual and specified with --qmask and
--hardmask.
--acceptall
Write the results of all alignments to output files. This option overrides all other
accept/reject options (including --id).
--allpairs_global filename
Perform optimal global pairwise alignments of the fasta sequences contained in filename.
Each sequence is compared to all sequencs that come after it in the file, resulting in a
total of n * (n-1) / 2 pairwise alignments, where n is the total number of sequences.
This command is multi-threaded.
--id real
Reject the sequence match if the pairwise identity is lower than real (value ranging from
0.0 to 1.0 included).
--threads positive integer
Number of computation threads to use (1 to 1024). The number of threads should be lesser
or equal to the number of available CPU cores. The default is to use all available
resources and to launch one thread per logical core.
--uc filename
Output pairwise alignment results in filename using a tab-separated uclust-like format
with 10 columns. Each sequence is compared to all other sequences, and all hits
(--acceptall) or only some hits (--id float) are reported, with one pairwise comparison
per line:
1. Record type, always set to 'H'.
2. Ordinal number of the target sequence (based on input order, starting from
zero).
3. Sequence length.
4. Percentage of similarity with the target sequence.
5. Match orientation, always set to '+'.
6. Not used, always set to zero.
7. Not used, always set to zero.
8. Compact representation of the pairwise alignment using the CIGAR format
(Compact Idiosyncratic Gapped Alignment Report): M (match/mismatch), D
(deletion) and I (insertion). The equal sign '=' indicates that the query is
identical to the centroid sequence.
9. Label of the query sequence.
10. Label of the target sequence.
Restriction site cutting options:
The input sequences in the file specified with the --cut command are cut into fragments at all
restriction sites matching the pattern given with the --cut_pattern option. The fragments on the
forward strand are written to the file specified with the --fastaout file and the fragments on the
reverse strand are written to the file specified with the --fastaout_rev option. Input sequences
that do not match are written to the file specified with the option --fastaout_discarded, and
their reverse complement are also written to the file specified with the --fastaout_discarded_rev
option. The relabel options (--relabel, --relabel_self, --relabel_keep, --relabel_md5, and
--relabel_sha1) may be used to relabel the output sequences).
--cut filename
Specify the input file with sequences in FASTA format.
--cut_pattern string
Specify the restriction site cutting pattern and positions. The pattern is a string of
lower- or uppercase letters specifying the nucleotides that must match, and may include
ambiguous nucleotide symbols. The special characters "^" (circumflex) and "_"
(underscore) are used to indicate the cutting position on the forward and reverse strand,
respectively. For example, the pattern "G^AATT_C" is the pattern for the EcoRI
restriction site. For such palindromic patterns (identical to its reverse complement) the
command will output all possible fragments on both strands. For non-palindromic sites, it
may be necessary to run the command also on the reverse complemented input sequences.
Exactly one cutting site on each strand must be indicated.
--fastaout filename
Specify the output file for the resulting fragments on the forward strand.
--fastaout_rev filename
Specify the output file for the resulting fragments on the reverse strand.
--fastaout_discarded filename
Specify the output file for the non-matching sequences.
--fastaout_discarded_rev filename
Specify the output file for the non-matching seqeunces, reverse complemented.
Searching options:
--alnout filename
Write pairwise global alignments to filename using a human-readable format. Use --rowlen
to modify alignment length. Output order may vary when using multiple threads.
--biomout filename
Write search results to an OTU table in the biom version 1.0 file format. The query file
contains the samples, while the database file contains the OTUs. Sample and OTU
identifiers are extracted from the header of these sequences. See the --biomout option in
the Clustering section for further details.
--blast6out filename
Write search results to filename using a blast-like tab-separated format of twelve fields
(listed below), with one line per query-target matching (or lack of matching if
--output_no_hits is used). Warning, vsearch uses global pairwise alignments, not blast's
seed-and-extend algorithm. Therefore, some common blast output values (alignment start
and end, evalue, bit score) are reported differently. Output order may vary when using
multiple threads. A similar output can be obtain with --userout filename and --userfields
query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits. A complete list and
description is available in the section 'Userfields' of this manual.
1. query: query label.
2. target: target (database sequence) label. The field is set to '*' if there is
no alignment.
3. id: percentage of identity (real value ranging from 0.0 to 100.0). The
percentage identity is defined as 100 * (matching columns) / (alignment length
- terminal gaps). See fields id0 to id4 for other definitions.
4. alnlen: length of the query-target alignment (number of columns). The field is
set to 0 if there is no alignment.
5. mism: number of mismatches in the alignment (zero or positive integer value).
6. opens: number of columns containing a gap opening (zero or positive integer
value, excluding terminal gaps).
7. qlo: first nucleotide of the query aligned with the target. Always equal to 1
if there is an alignment, 0 otherwise (see qilo to ignore initial gaps).
8. qhi: last nucleotide of the query aligned with the target. Always equal to the
length of the pairwise alignment, 0 otherwise (see qihi to ignore terminal
gaps).
9. tlo: first nucleotide of the target aligned with the query. Always equal to 1
if there is an alignment, 0 otherwise (see tilo to ignore initial gaps).
10. thi: last nucleotide of the target aligned with the query. Always equal to the
length of the pairwise alignment, 0 otherwise (see tihi to ignore terminal
gaps).
11. evalue: expectancy-value (not computed for nucleotide alignments). Always set
to -1.
12. bits: bit score (not computed for nucleotide alignments). Always set to 0.
--db filename
Compare query sequences (specified with --usearch_global) to the target sequences
contained in filename in FASTA or FASTQ format, using global pairwise alignment.
Alternatively, the name of a preformatted UDB database created using the makeudb_usearch
command (see below) may be specified.
--dbmask none|dust|soft
Mask regions in the target database sequences using the dust method or the soft method,
or do not mask (none). Warning, when using soft masking search commands become case
sensitive. The default is to mask using dust.
--dbmatched filename
Write database target sequences matching at least one query sequence to filename, in
fasta format. If the option --sizeout is used, the number of queries that matched each
target sequence is indicated using the pattern ";size=integer;".
--dbnotmatched filename
Write database target sequences not matching query sequences to filename, in fasta
format.
--fastapairs filename
Write pairwise alignments of query and target sequences to filename, in fasta format.
--fulldp Dummy option for compatibility with usearch. To maximize search sensitivity, vsearch uses
a 8-way 16-bit SIMD vectorized full dynamic programming algorithm (Needleman-Wunsch),
whether or not --fulldp is specified.
--gapext string
Set penalties for a gap extension. See --gapopen for a complete description of the
penalty declaration system. The default is to initialize the six gap extending penalties
using a penalty of 2 for extending internal gaps and a penalty of 1 for extending
terminal gaps, in both query and target sequences (i.e. 2I/1E).
--gapopen string
Set penalties for a gap opening. A gap opening can occur in six different contexts: in
the query (Q) or in the target (T) sequence, at the left (L) or right (R) extremity of
the sequence, or inside the sequence (I). Sequence symbols (Q and T) can be combined with
location symbols (L, I, and R), and numerical values to declare penalties for all
possible contexts: aQL/bQI/cQR/dTL/eTI/fTR, where abcdef are zero or positive integers,
and '/' is used as a separator.
To simplify declarations, the location symbols (L, I, and R) can be combined, the symbol
(E) can be used to treat both extremities (L and R) equally, and the symbols Q and T can
be omitted to treat query and target sequences equally. For instance, the default is to
declare a penalty of 20 for opening internal gaps and a penalty of 2 for opening terminal
gaps (left or right), in both query and target sequences (i.e. 20I/2E). If only a
numerical value is given, without any sequence or location symbol, then the penalty
applies to all gap openings. To forbid gap-opening, an infinite penalty value can be
declared with the symbol '*'. To use vsearch as a semi-global aligner, a null-penalty can
be applied to the left (L) or right (R) gaps.
vsearch always initializes the six gap opening penalties using the default parameters
(20I/2E). The user is then free to declare only the values he/she wants to modify. The
string is scanned from left to right, accepted symbols are (0123456789/LIREQT*), and
later values override previous values.
Please note that vsearch, in contrast to usearch, only allows integer gap penalties.
Because the lowest gap penalties are 0.5 by default in usearch, all default scores and
gap penalties in vsearch have been doubled to maintain equivalent penalties and to
produce identical alignments.
--hardmask
Mask sequence regions by replacing them with Ns instead of setting them to lower case as
is the default. For more information, please see the Masking section.
--id real
Reject the sequence match if the pairwise identity is lower than real (value ranging from
0.0 to 1.0 included). The search process sorts target sequences by decreasing number of
k-mers they have in common with the query sequence, using that information as a proxy for
sequence similarity. That efficient pre-filtering also prevents pairwise alignments with
weakly matching targets, as there needs to be at least 6 shared k-mers to start the
pairwise alignment, and at least one out of every 16 k-mers from the query needs to match
the target. Consequently, using values lower than --id 0.5 is not likely to capture more
weakly matching targets. The pairwise identity is by default defined as the number of
(matching columns) / (alignment length - terminal gaps). That definition can be modified
by --iddef.
--iddef 0|1|2|3|4
Change the pairwise identity definition used in --id. Values accepted are:
0. CD-HIT definition: (matching columns) / (shortest sequence length).
1. edit distance: (matching columns) / (alignment length).
2. edit distance excluding terminal gaps (default definition for --id).
3. Marine Biological Lab definition counting each gap opening (internal or
terminal) as a single mismatch, whether or not the gap was extended: 1.0 -
[(mismatches + gap openings)/(longest sequence length)]
4. BLAST definition, equivalent to --iddef 1 for global pairwise alignments.
The option --userfields accepts the fields id0 to id4, in addition to the field id, to
report the pairwise identity values corresponding to the different definitions.
--idprefix positive integer
Reject the sequence match if the first integer nucleotides of the target do not match the
query.
--idsuffix positive integer
Reject the sequence match if the last integer nucleotides of the target do not match the
query.
--lca_cutoff real
Adjust the fraction of matching hits required for the last common ancestor (LCA) output
with the --lcaout option during searches. The default value is 1.0 which requires all
hits to match at each taxonomic rank for that rank to be included. If a lower cutoff
value is used, e.g. 0.95, a small fraction of non-matching hits are allowed while that
rank will still be reported. The argument to this option must be larger than 0.5, but not
larger than 1.0.
--lcaout filename
Output last common ancestor (LCA) information about the hits of each query to a text file
in a tab-separated format. The first column contains the query id, while the second
column contains the taxonomic information. The headers of the sequences in the database
must contain taxonomic information in the same format as used with the --sintax command,
e.g. "tax=k:Archaea,p:Euryarchaeota,c:Halobacteria". Only the initial parts of the
taxonomy that are common to a large fraction of the hits of each query will be output. It
is necessary to set the --maxaccepts option to a value different from 1 for this
information to be useful. The --top_hits_only option may also be useful. The fraction of
matching hits required may be adjusted by the --lca_cutoff option (default 1.0).
--leftjust
Reject the sequence match if the pairwise alignment begins with gaps.
--lengthout
Write sequence length information to the output files in FASTA format by adding a
";length=integer" attribute in the header.
--match integer
Score assigned to a match (i.e. identical nucleotides) in the pairwise alignment. The
default value is 2.
--matched filename
Write query sequences matching database target sequences to filename, in fasta format.
--maxaccepts positive integer
Maximum number of matching target sequences to accept before stopping the search for a
given query. The default value is 1. This option works in pair with --maxrejects. The
search process sorts target sequences by decreasing number of k-mers they have in common
with the query sequence, using that information as a proxy for sequence similarity. After
pairwise alignments, if the first target sequence passes the acceptation criteria, it is
accepted as best hit and the search process stops for that query. If --maxaccepts is set
to a higher value, more matching targets are accepted. If --maxaccepts and --maxrejects
are both set to 0, the complete database is searched. See --maxhits option for a control
on the number of hits reported per query when search is done on both strands.
--maxdiffs positive integer
Reject the sequence match if the alignment contains at least integer substitutions,
insertions or deletions.
--maxgaps positive integer
Reject the sequence match if the alignment contains at least integer insertions or
deletions.
--maxhits non-negative integer
Maximum number of hits to show once the search is terminated for a given query (hits are
sorted by decreasing identity). When searching only on the plus strand (default
situation, see --strand), the number of matching targets (--maxaccepts) and the number of
hits (--maxhits) are the same. However, when searching on both strands, there could be
two hits per target (one per strand): --maxhits then controls the overall number of
reported hits per query. Unlimited by default or if the argument is zero. This option
applies to --alnout, --blast6out, --fastapairs, --samout, --uc, or --userout output
files.
--maxid real
Reject the sequence match if the percentage of identity between the two sequences is
greater than real.
--maxqsize positive integer
Reject query sequences with an abundance greater than integer.
--maxqt real
Reject if the query/target sequence length ratio is greater than real.
--maxrejects positive integer
Maximum number of non-matching target sequences to consider before stopping the search
for a given query. The default value is 32. This option works in pair with --maxaccepts.
The search process sorts target sequences by decreasing number of k-mers they have in
common with the query sequence, using that information as a proxy for sequence
similarity. After pairwise alignments, if none of the first 32 examined target sequences
pass the acceptation criteria, the search process stops for that query (no hit). If
--maxrejects is set to a higher value, more target sequences are considered. If
--maxaccepts and --maxrejects are both set to 0, the complete database is searched.
--maxsizeratio real
Reject if the query/target abundance ratio is greater than real.
--maxsl real
Reject if the shorter/longer sequence length ratio is greater than real.
--maxsubs positive integer
Reject the sequence match if the pairwise alignment contains more than integer
substitutions.
--mid real
Reject the sequence match if the percentage of identity is lower than real (ignoring all
gaps, internal and terminal).
--mincols positive integer
Reject the sequence match if the alignment length is shorter than integer.
--minqt real
Reject if the query/target sequence length ratio is lower than real.
--minsizeratio real
Reject if the query/target abundance ratio is lower than real.
--minsl real
Reject if the shorter/longer sequence length ratio is lower than real.
--mintsize positive integer
Reject target sequences with an abundance lower than integer.
--minwordmatches non-negative integer
Minimum number of word matches required for a sequence to be considered further. Default
value is 12 for the default word length 8. For word lengths 3-15, the default minimum
word matches are 18, 17, 16, 15, 14, 12, 11, 10, 9, 8, 7, 5 and 3, respectively. If the
query sequence has fewer unique words than the number specified, all words in the query
must match. If the argument is 0, no word matches are required.
--mismatch integer
Score assigned to a mismatch (i.e. different nucleotides) in the pairwise alignment. The
default value is -4.
--mothur_shared_out filename
Write search results to an OTU table in the mothur 'shared' tab-separated plain text file
format. The query file contains the samples, while the database file contains the OTUs.
Sample and OTU identifiers are extracted from the header of these sequences. See the
--otutabout option in the Clustering section for further details.
--notmatched filename
Write query sequences not matching database target sequences to filename, in fasta
format.
--otutabout filename
Write search results to an OTU table in the classic tab-separated plain text format. The
query file contains the samples, while the database file contains the OTUs. Sample and
OTU identifiers are extracted from the header of these sequences. See the
--mothur_shared_out option in the Clustering section for further details.
--output_no_hits
Write both matching and non-matching queries to --alnout, --blast6out, --samout or
--userout output files. Non-matching queries are labelled 'No hits' in --alnout files.
--pattern string
This option is ignored. It is provided for compatibility with usearch.
--qmask none|dust|soft
Mask regions in the query sequences using the dust or the soft algorithms, or do not mask
(none). Warning, when using soft masking search commands become case sensitive. The
default is to mask using dust.
--qsegout filename
Write the aligned part of each query sequence to filename in FASTA format.
--query_cov real
Reject if the fraction of the query aligned to the target sequence is lower than real
(value ranging from 0.0 to 1.0 included). The query coverage is computed as (matches +
mismatches) / query sequence length. Internal or terminal gaps are not taken into
account.
--rightjust
Reject the sequence match if the pairwise alignment ends with gaps.
--rowlen positive integer
Width of alignment lines in --alnout output. The default value is 64. Set to 0 to
eliminate wrapping.
--samheader
Include header lines to the SAM file when --samout is specified. The header includes
lines starting with @HD, @SQ and @PG, but no @RG lines (see (link) ⟨https://github.com/
samtools/hts-specs⟩ <https://github.com/samtools/hts-specs>). By default no header line
is written.
--samout filename
Write alignment results to filename using the SAM format (a tab-separated text file).
When using the --samheader option, the SAM file starts with header lines. Each non-header
line is a SAM record, which represents either a query-target alignment or the absence of
match for a query (output order may vary when using multiple threads). Each record
contains 11 mandatory fields and optional fields (see (link) ⟨https://github.com/
samtools/hts-specs⟩ <https://github.com/samtools/hts-specs> for a complete description of
the format):
1. query sequence label.
2. combination of bitwise flags. Possible values are: 0 (top hit), 4 (no hit), 16
(reverse-complemented hit), 256 (secondary hit, i.e. all hits except the top
hit).
3. target sequence label.
4. first position of a target aligned with the query (always 1 for global
pairwise alignments, 0 if there is no match).
5. mapping quality (ignored, always set to '*').
6. CIGAR string (set to '*' if there is no match).
7. name of the target sequence matching with the next read of the query (for mate
reads only, ignored and always set to '*').
8. position of the primary alignment of the next read of the query (for mate
reads only, ignored and always set to 0).
9. target sequence length (for multi-segment targets, ignored and always set to
0).
10. query sequence (complete, not only the segment aligned to the target as
usearch does).
11. quality string (ignored, always set to '*').
Optional fields for query-target matches (number and order of fields may vary):
12. AS:i:? alignment score (i.e. percentage of identity).
13. XN:i:? next best alignment score (always set to 0).
14. XM:i:? number of mismatches.
15. XO:i:? number of gap openings (excluding terminal gaps).
16. XG:i:? number of gap extensions (excluding terminal gaps).
17. NM:i:? edit distance to the target (sum of XM and XG).
18. MD:Z:? string for mismatching positions.
19. YT:Z:UU string representing the alignment type.
--search_exact filename
Search for exact full-length matches to the query sequences contained in filename in the
database of target sequences (--db). Only 100% exact matches are reported and this
command is much faster than --usearch_global. The --id, --maxaccepts and --maxrejects
options are ignored, but the rest of the searching options may be specified.
--self Reject the sequence match if the query and target labels are identical.
--selfid Reject the sequence match if the query and target sequences are strictly identical.
--sizeout
Add abundance annotations to the output of the option --dbmatched (using the pattern
';size=integer;'), to report the number of queries that matched each target.
--strand plus|both
When searching for similar sequences, check the plus strand only (default) or check both
strands.
--target_cov real
Reject the sequence match if the fraction of the target sequence aligned to the query
sequence is lower than real. The target coverage is computed as (matches + mismatches) /
target sequence length. Internal or terminal gaps are not taken into account.
--top_hits_only
Only the top hits with an equally high percentage of identity between the query and
database sequence sets are written to the output specified with the options --lcaout,
--alnout, --samout, --userout, --blast6out, --uc, --fastapairs, --matched or --notmatched
(but not --dbmatched and --dbnotmatched). For each query, the top hit is the one
presenting the highest percentage of identity (see the --iddef option to change the way
identity is measured). For a given query, if several top hits present exactly the same
percentage of identity, the number of matching targets reported is controlled by the
--maxaccepts value (1 by default), and the number of hits is controlled by the --maxhits
option.
--tsegout filename
Write the aligned part of each target sequence to filename in FASTA format.
--uc filename
Output searching results in filename using a tab-separated uclust-like format with 10
columns. When using the --search_exact command, the table layout is the same than with
the --allpairs_global. When using the --usearch_global command, the table present two
different type of entries: hit (H) or no hit (N). Each query sequence is compared to all
other sequences, and the best hit (--maxaccept 1) or several hits (--maxaccept > 1) are
reported (H). Output order may vary when using multiple threads. Column content varies
with the type of entry (H or N):
1. Record type: H, or N ('hit' or 'no hit').
2. Ordinal number of the target sequence (based on input order, starting from
zero). Set to '*' for N.
3. Sequence length. Set to '*' for N.
4. Percentage of similarity with the target sequence. Set to '*' for N.
5. Match orientation + or -. . Set to '.' for N.
6. Not used, always set to zero for H, or '*' for N.
7. Not used, always set to zero for H, or '*' for N.
8. Compact representation of the pairwise alignment using the CIGAR format
(Compact Idiosyncratic Gapped Alignment Report): M (match/mismatch), D
(deletion) and I (insertion). The equal sign '=' indicates that the query is
identical to the centroid sequence. Set to '*' for N.
9. Label of the query sequence.
10. Label of the target centroid sequence. Set to '*' for N.
--uc_allhits
When using the --uc option, show all hits, not just the top hit for each query.
--usearch_global filename
Compare target sequences (--db) to the query sequences contained in filename in FASTA or
FASTQ format, using global pairwise alignment.
--userfields string
When using --userout, select and order the fields written to the output file. Fields are
separated by '+' (e.g. query+target+id). See the 'Userfields' section for a complete list
of fields.
--userout filename
Write user-defined tab-separated output to filename. Select the fields with the option
--userfields. Output order may vary when using multiple threads. If --userfields is empty
or not present, filename is empty.
--weak_id real
Show hits with percentage of identity of at least real, without terminating the search. A
normal search stops as soon as enough hits are found (as defined by --maxaccepts,
--maxrejects, and --id). As --weak_id reports weak hits that are not deduced from
--maxaccepts, high --id values can be used, hence preserving both speed and sensitivity.
Logically, real must be smaller than the value indicated by --id.
--wordlength positive integer
Length of words (i.e. k-mers) for database indexing. The range of possible values goes
from 3 to 15, but values near 8 or 9 are generally recommended. Longer words may reduce
the sensitivity/recall for weak similarities, but can increase precision. On the other
hand, shorter words may increase sensitivity or recall, but may reduce precision.
Computation time generally increases with shorter words and decreases with longer words,
but it increases again for very long words. Memory requirements for a part of the index
increase with a factor of 4 each time word length increases by one nucleotide, and this
generally becomes significant for long words (12 or more). The default value is 8.
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
Shuffling options:
Fasta entries in the input file are outputted in a pseudo-random order.
--lengthout
Write sequence length information to the output files in FASTA format by adding a
";length=integer" attribute in the header.
--output filename
Write the shuffled sequences to filename, in fasta format.
--randseed positive integer
When shuffling sequence order, use integer as seed. A given seed always produces the same
output order (useful for replicability). Set to 0 to use a pseudo-random seed (default
behaviour).
--relabel string
Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the
new headers. Use --sizeout to conserve the abundance annotations.
--relabel_keep
When relabelling, keep the old identifier in the header after a space.
--relabel_md5
Relabel sequences using the MD5 message digest algorithm applied to each sequence. Former
sequence headers are discarded. The sequence is converted to upper case and U is replaced
by T before the digest is computed. The MD5 digest is a cryptographic hash function
designed to minimize the probability that two different inputs gives the same output,
even for very similar, but non-identical inputs. Still, there is always a very small, but
non-zero probability that two different inputs give the same result. The MD5 digest
generates a 128-bit (16-byte) digest that is represented by 16 hexadecimal numbers (using
32 symbols among 0123456789abcdef). Use --sizeout to conserve the abundance annotations.
--relabel_self
Relabel sequences using the sequence itself as the label.
--relabel_sha1
Relabel sequences using the SHA1 message digest algorithm applied to each sequence. It is
similar to the --relabel_md5 option but uses the SHA1 algorithm instead of the MD5
algorithm. The SHA1 digest generates a 160-bit (20-byte) result that is represented by 20
hexadecimal numbers (40 symbols). The probability of a collision (two non-identical
sequences having the same digest) is smaller for the SHA1 algorithm than it is for the
MD5 algorithm. Use --sizeout to conserve the abundance annotations.
--sizeout
When using --relabel, --relabel_self, --relabel_md5 or --relabel_sha1, preserve and
report abundance annotations to the output fasta file (using the pattern
';size=integer;').
--shuffle filename
Pseudo-randomly shuffle the order of sequences contained in filename.
--topn positive integer
Output only the first integer sequences after pseudo-random reordering.
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
--xsize Strip abundance information from the headers when writing the output file.
Sorting options:
Fasta entries are sorted by decreasing abundance (--sortbysize) or sequence length
(--sortbylength). To obtain a stable sorting order, ties are sorted by decreasing abundance and
label increasing alpha-numerical order (--sortbylength), or just by label increasing alpha-
numerical order (--sortbysize). Label sorting assumes that all sequences have unique labels. The
same applies to the automatic sorting performed during chimera checking (--uchime_denovo),
dereplication (--derep_fulllength), and clustering (--cluster_fast and --cluster_size).
--lengthout
Write sequence length information to the output files in FASTA format by adding a
";length=integer" attribute in the header.
--maxsize positive integer
When using --sortbysize, discard sequences with an abundance value greater than integer.
--minsize positive integer
When using --sortbysize, discard sequences with an abundance value smaller than integer.
--output filename
Write the sorted sequences to filename, in fasta format.
--relabel string
Please see the description of the same option under Chimera detection for details.
--relabel_keep
When relabelling, keep the old identifier in the header after a space.
--relabel_md5
Please see the description of the same option under Chimera detection for details.
--relabel_self
Please see the description of the same option under Chimera detection for details.
--relabel_sha1
Please see the description of the same option under Chimera detection for details.
--sizeout
When using --relabel, report abundance annotations to the output fasta file (using the
pattern ';size=integer;').
--sortbylength filename
Sort by decreasing length the sequences contained in filename. See the general options
--minseqlength and --maxseqlength to eliminate short and long sequences.
--sortbysize filename
Sort by decreasing abundance the sequences contained in filename (missing abundance
values are assumed to be ';size=1'). See the options --minsize and --maxsize to eliminate
rare and dominant sequences.
--topn positive integer
Output only the top integer sequences (i.e. the longest or the most abundant).
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
--xsize Strip abundance information from the headers when writing the output file.
Subsampling options:
Subsampling randomly extracts a certain number or a certain percentage of the sequences in the
input file. If the --sizein option is in effect, the abundances of the input sequences is taken
into account and the sampling is performed as if the input sequences were rereplicated, subsampled
and dereplicated before being written to the output file. The extraction is performed as a random
sampling with a uniform distribution among the input sequences and is performed without
replacement. The input file is specified with the --fastx_subsample option, the output files are
specified with the --fastaout and --fastqout options and the amount of sequences to be sampled is
specified with the --sample_pct or --sample_size options. The sequences not sampled may be written
to files specified with the options --fasta_discarded and --fastq_discarded. The --fastq_ascii,
--fastq_qmin and --fastq_qmax options are also available.
--fastaout filename
Write the sampled sequences to filename, in fasta format.
--fastaout_discarded filename
Write the sequences not sampled to filename, in fasta format.
--fastq_ascii positive integer
Define the ASCII character number used as the basis for the FASTQ quality score. The
default is 33, which is used by the Sanger / Illumina 1.8+ FASTQ format (phred+33). The
value 64 is used by the Solexa, Illumina 1.3+ and Illumina 1.5+ formats (phred+64). Only
33 and 64 are valid arguments.
--fastq_qmax positive integer
Specify the maximum quality score accepted when reading FASTQ files. The default is 41,
which is usual for recent Sanger/Illumina 1.8+ files.
--fastq_qmin positive integer
Specify the minimum quality score accepted for FASTQ files. The default is 0, which is
usual for recent Sanger/Illumina 1.8+ files. Older formats may use scores between -5 and
2.
--fastqout filename
Write the sampled sequences to filename, in fastq format. Requires input in fastq format.
--fastqout_discarded filename
Write the sequences not sampled to filename, in fastq format. Requires input in fastq
format.
--fastx_subsample filename
Perform subsampling from the sequences in the specified input file that is in FASTA or
FASTQ format.
--lengthout
Write sequence length information to the output files in FASTA format by adding a
";length=integer" attribute in the header.
--randseed positive integer
Use integer as a seed for the pseudo-random generator. A given seed always produces the
same output, which is useful for replicability. Set to 0 to use a pseudo-random seed
(default behaviour).
--relabel string
Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the
new headers. Use --sizeout to conserve the abundance annotations.
--relabel_keep
When relabelling, keep the old identifier in the header after a space.
--relabel_md5
Relabel sequences using the MD5 message digest algorithm applied to each sequence. Former
sequence headers are discarded. The sequence is converted to upper case and U is replaced
by T before the digest is computed. The MD5 digest is a cryptographic hash function
designed to minimize the probability that two different inputs give the same output, even
for very similar, but non-identical inputs. Still, there is always a very small, but non-
zero probability that two different inputs give the same result. The MD5 digest generates
a 128-bit (16-byte) digest that is represented by 16 hexadecimal numbers (using 32
symbols among 0123456789abcdef). Use --sizeout to conserve the abundance annotations.
--relabel_self
Relabel sequences using the sequence itself as the label.
--relabel_sha1
Relabel sequences using the SHA1 message digest algorithm applied to each sequence. It is
similar to the --relabel_md5 option but uses the SHA1 algorithm instead of the MD5
algorithm. The SHA1 digest generates a 160-bit (20-byte) result that is represented by 20
hexadecimal numbers (40 symbols). The probability of a collision (two non-identical
sequences having the same digest) is smaller for the SHA1 algorithm than it is for the
MD5 algorithm. Use --sizeout to conserve the abundance annotations.
--sample_pct real
Subsample the given percentage of the input sequences. Accepted values range from 0.0 to
100.0.
--sample_size positive integer
Extract the given number of sequences.
--sizein Take the abundance information of the input file into account, otherwise the abundance of
each sequence is considered to be 1.
--sizeout
Write abundance information to the output file.
--xlength
Strip header attribute ";length=integer" from input sequences. This attribute is added to
output sequences by the --lengthout option.
--xsize Strip abundance information from the headers when writing the output file.
Taxonomic classification options:
The vsearch command --sintax will classify the input sequences according to the Sintax algorithm
as described by Robert Edgar (2016) in SINTAX: a simple non-Bayesian taxonomy classifier for 16S
and ITS sequences, BioRxiv, 074161. Preprint. doi: 10.1101/074161 (link) ⟨https://doi.org/10.1101/
074161⟩
The name of the fasta file containing the input sequences to be classified is given as an argument
to the --sintax command. The reference sequence database is specified with the --db option. The
results are written in a tab delimited text file whose name is specified with the --tabbedout
option. The --sintax_cutoff option may be used to set a minimum level of bootstrap support for the
taxonomic ranks to be reported. The `--randseed` option may be included to specify a seed for
initialisation of the random number generator used by the algorithm. Please note that when using
multiple threads, the `--randseed` option may not work as intended, because sequences may be
processed in a random order by different threads. To ensure the same results each time, use a
single thread (`--threads 1`) in combination with a fixed random seed specified with `--randseed`.
Multithreading is supported. Databases in UDB files are supported. The strand option may be
specified.
The reference database must contain taxonomic information in the header of each sequence in the
form of a string starting with ";tax=" and followed by a comma-separated list of up to eight
taxonomic identifiers. Each taxonomic identifier must start with an indication of the rank by one
of the letters d (for domain) k (kingdom), p (phylum), c (class), o (order), f (family), g
(genus), or s (species). The letter is followed by a colon (:) and the name of that rank. Commas
and semicolons are not allowed in the name of the rank.
Example: ">X80725_S000004313;tax=d:Bacteria,p:Proteobacteria,c:Gammaproteobacteria,
o:Enterobacteriales,f:Enterobacteriaceae,g:Escherichia/Shigella,s:Escherichia_coli".
The option --notrunclabels is turned on by default for this command, allowing spaces in the
taxonomic identifiers.
--db filename
Read the reference sequences from filename, in FASTA, FASTQ or UDB format. These
sequences need to be annotated with taxonomy.
--randseed positive integer
Use integer as seed for the random number generator used in the Sintax algorithm. A given
seed always produces the same output order (useful for replicability). Set to 0 to use a
pseudo-random seed (default behaviour). Does not work correctly with multiple threads;
please use `--threads 1` to ensure correct behaviour.
--sintax_cutoff real
Specify a minimum level of bootstrap support for the taxonomic ranks that will be
included in column 4 of the output file. For instance 0.9, corresponding to 90%.
--sintax filename
Read the input sequences from filename, in FASTA or FASTQ format.
--tabbedout filename
Write the results to filename, in a tab-separated text format. Column 1 contains the
query label. Column 2 contains the predicted taxonomy in the same format as for the
reference data, with bootstrap support indicated in parentheses after each rank. Column 3
contains the strand. If the --sintax_cutoff option is used, the predicted taxonomy will
be repeated in column 4 while omitting the bootstrap values and including only the ranks
with support at or above the threshold.
UDB options:
Databases to be used with the --usearch_global command may be prepared from FASTA files and stored
to a binary UDB formatted file in order to speed up searching. This may be worthwhile when
searching a large database repeatedly. The sequences are indexed and stored in a way that can be
quickly loaded into memory. The commands and options below can be used to create and inspect UDB
files. An UDB file may be specified with the --db option instead of a FASTA formatted file with
the --usearch_global command.
--dbmask none|dust|soft
Specify the sequence masking method used with the --makeudb_usearch command, either none,
dust or soft. No masking is performed when none is specified. When dust is specified, the
DUST algorithm will be used for masking low complexity regions (short repeats and skewed
composition). Lower case letters in the input file will be masked when soft is specified
(soft masking).
--hardmask
Mask sequences by replacing letters with N for the --makeudb_usearch command. The default
is to use lower case letters (soft masking).
--makeudb_usearch filename
Create an UDB database file from the FASTA-formatted sequences in the file with the given
filename. The UDB database is written to the file specified with the --output option.
--output filename
Specify the filename of a FASTA or UDB output file for the --makeudb_usearch or the
--udb2fasta command, respectively.
--udb2fasta filename
Read the UDB database in the file with the given filename and output the sequences in
FASTA format in the file specified by the --output option.
--udbinfo filename
Show information about the UDB database in the file with the given filename.
--udbstats filename
Report statistics about the indexed words in the UDB database in the file with the given
filename.
--wordlength positive integer
Specify the length of the words to be used when creating the UDB database index using the
--makeudb_usearch command. Valid numbers range from 3 to 15. The default is 8.
Userfields (fields accepted by the --userfields option):
aln Print a string of M (match/mismatch, i.e. not a gap), D (delete, i.e. a gap in the query)
and I (insert, i.e. a gap in the target) representing the pairwise alignment. Empty field
if there is no alignment.
alnlen Print the length of the query-target alignment (number of columns). The field is set to 0
if there is no alignment.
bits Bit score (not computed for nucleotide alignments). Always set to 0.
caln Compact representation of the pairwise alignment using the CIGAR format (Compact
Idiosyncratic Gapped Alignment Report): M (match/mismatch), D (deletion) and I
(insertion). Empty field if there is no alignment.
evalue E-value (not computed for nucleotide alignments). Always set to -1.
exts Number of columns containing a gap extension (zero or positive integer value).
gaps Number of columns containing a gap (zero or positive integer value, excluding terminal
gaps).
id The percentage of identity, according to the identity definition specified by the --iddef
option. Equal to id0, id1, id2, id3 or id4 below. By default the same as id2.
id0 CD-HIT definition of the percentage of identity (real value ranging from 0.0 to 100.0)
using the length of the shortest sequence in the pairwise alignment as denominator: 100 *
(matching columns) / (shortest sequence length).
id1 The percentage of identity (real value ranging from 0.0 to 100.0) is defined as the edit
distance: 100 * (matching columns) / (alignment length).
id2 The percentage of identity (real value ranging from 0.0 to 100.0) is defined as the edit
distance, excluding terminal gaps.
id3 Marine Biological Lab definition of the percentage of identity (real value ranging from
0.0 to 100.0), counting each gap opening (internal or terminal) as a single mismatch,
whether or not the gap was extended, and using the length of the longest sequence in the
pairwise alignment as denominator: 100 * (1.0 - [(mismatches + gaps) / (longest sequence
length)]).
id4 BLAST definition of the percentage of identity (real value ranging from 0.0 to 100.0),
equivalent to --iddef 1 in a context of global pairwise alignment. The field id4 is
always equal to the field id1.
ids Number of matches in the alignment (zero or positive integer value).
mism Number of mismatches in the alignment (zero or positive integer value).
opens Number of columns containing a gap opening (zero or positive integer value, excluding
terminal gaps).
pairs Number of columns containing only nucleotides. That value corresponds to the length of
the alignment minus the gap-containing columns (zero or positive integer value).
pctgaps Number of columns containing gaps expressed as a percentage of the alignment length (real
value ranging from 0.0 to 100.0).
pctpv Percentage of positive columns. When working with nucleotide sequences, this is
equivalent to the percentage of matches (real value ranging from 0.0 to 100.0).
pv Number of positive columns. When working with nucleotide sequences, this is equivalent to
the number of matches (zero or positive integer value).
qcov Fraction of the query sequence that is aligned with the target sequence (real value
ranging from 0.0 to 100.0). The query coverage is computed as 100.0 * (matches +
mismatches) / query sequence length. Internal or terminal gaps are not taken into
account. The field is set to 0.0 if there is no alignment.
qframe Query frame (-3 to +3). That field only concerns coding sequences and is not computed by
vsearch. Always set to +0.
qhi Last nucleotide of the query aligned with the target. Always equal to the length of the
pairwise alignment, 0 otherwise (see qihi to ignore terminal gaps).
qihi Last nucleotide of the query aligned with the target (ignoring terminal gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.
qilo First nucleotide of the query aligned with the target (ignoring initial gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.
ql Query sequence length (positive integer value). The field is set to 0 if there is no
alignment.
qlo First nucleotide of the query aligned with the target. Always equal to 1 if there is an
alignment, 0 otherwise (see qilo to ignore initial gaps).
qrow Print the sequence of the query segment as seen in the pairwise alignment (i.e. with gap
insertions if need be). Empty field if there is no alignment.
qs Query segment length. Always equal to query sequence length.
qstrand Query strand orientation (+ or - for nucleotide sequences). Empty field if there is no
alignment.
query Query label.
raw Raw alignment score (negative, null or positive integer value). The score is the sum of
match rewards minus mismatch penalties, gap openings and gap extensions. The field is set
to 0 if there is no alignment.
target Target label. The field is set to '*' if there is no alignment.
tcov Fraction of the target sequence that is aligned with the query sequence (real value
ranging from 0.0 to 100.0). The target coverage is computed as 100.0 * (matches +
mismatches) / target sequence length. Internal or terminal gaps are not taken into
account. The field is set to 0.0 if there is no alignment.
tframe Target frame (-3 to +3). That field only concerns coding sequences and is not computed by
vsearch. Always set to +0.
thi Last nucleotide of the target aligned with the query. Always equal to the length of the
pairwise alignment, 0 otherwise (see tihi to ignore terminal gaps).
tihi Last nucleotide of the target aligned with the query (ignoring terminal gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.
tilo First nucleotide of the target aligned with the query (ignoring initial gaps). Nucleotide
numbering starts from 1. The field is set to 0 if there is no alignment.
tl Target sequence length (positive integer value). The field is set to 0 if there is no
alignment.
tlo First nucleotide of the target aligned with the query. Always equal to 1 if there is an
alignment, 0 otherwise (see tilo to ignore initial gaps).
trow Print the sequence of the target segment as seen in the pairwise alignment (i.e. with gap
insertions if need be). Empty field if there is no alignment.
ts Target segment length. Always equal to target sequence length. The field is set to 0 if
there is no alignment.
tstrand Target strand orientation (+ or - for nucleotide sequences). Always set to '+', so
reverse strand matches have tstrand '+' and qstrand '-'. Empty field if there is no
alignment.
DELIBERATE CHANGES
If you are a usearch user, our objective is to make you feel at home. That's why vsearch was designed to
behave like usearch, to some extent. Like any complex software, usearch is not free from quirks and
inconsistencies. We decided not to reproduce some of them, and for complete transparency, to document
here the deliberate changes we made.
During a search with usearch, when using the options --blast6out and --output_no_hits, for queries with
no match the number of fields reported is 13, where it should be 12. This is corrected in vsearch.
The field raw of the --userfields option is not informative in usearch. This is corrected in vsearch.
The fields qlo, qhi, tlo, thi now have counterparts (qilo, qihi, tilo, tihi) reporting alignment
coordinates ignoring terminal gaps.
In usearch, when using the option --output_no_hits, queries that receive no match are reported in
--blast6out file, but not in the alignment output file. This is corrected in vsearch.
vsearch introduces a new --cluster_size command that sorts sequences by decreasing abundance before
clustering.
vsearch reintroduces --iddef alternative pairwise identity definitions that were removed from usearch.
vsearch extends the --topn option to sorting commands.
vsearch extends the --sizein option to dereplication (--derep_fulllength) and clustering
(--cluster_fast).
vsearch treats T and U as identical nucleotides during dereplication.
vsearch sorting is stabilized by using sequence abundances or sequences labels as secondary or tertiary
keys.
vsearch by default uses the DUST algorithm for masking low-complexity regions. Masking behaviour is also
slightly changed to be more consistent.
NOVELTIES
vsearch introduces new commands and new options not present in usearch 7. They are described in the
'Options' section of this manual. Here is a short list:
- uchime2_denovo, uchime3_denovo, alignwidth, borderline, fasta_score (chimera checking)
- cluster_size, cluster_unoise, clusterout_id, clusterout_sort, profile (clustering)
- fasta_width, gzip_decompress, bzip2_decompress (general option)
- iddef (clustering, pairwise alignment, searching)
- maxuniquesize (dereplication)
- relabel_md5, relabel_self and relabel_sha1 (chimera detection, dereplication, FASTQ processing,
shuffling, sorting)
- shuffle (shuffling)
- fastq_eestats, fastq_eestats2, fastq_maxlen, fastq_truncee (FASTQ processing)
- fastaout_discarded, fastqout_discarded (subsampling)
- rereplicate (dereplication/rereplication)
EXAMPLES
Align all sequences in a database with each other and output all pairwise alignments:
vsearch --allpairs_global database.fas --alnout results.aln --acceptall
Check for the presence of chimeras (de novo); parents should be at least 1.5 times more abundant than
chimeras. Output non-chimeric sequences in fasta format (no wrapping):
vsearch --uchime_denovo queries.fas --abskew 1.5 --nonchimeras results.fas --fasta_width 0
Cluster with a 97% similarity threshold, collect cluster centroids, and write cluster descriptions using
a uclust-like format:
vsearch --cluster_fast queries.fas --id 0.97 --centroids centroids.fas --uc clusters.uc
Dereplicate the sequences contained in queries.fas, take into account the abundance information already
present, write unwrapped fasta sequences to queries_unique.fas with the new abundance information,
discard all sequences with an abundance of 1:
vsearch --derep_fulllength queries.fas --sizein --fasta_width 0 --sizeout --output
queries_unique.fas --minuniquesize 2
Mask simple repeats and low complexity regions in the input fasta file with the DUST algorithm (masked
regions are lowercased), and write the results to the output file:
vsearch --maskfasta queries.fas --qmask dust --output queries_masked.fas
Search queries in a reference database, with a 80%-similarity threshold, take terminal gaps into account
when calculating pairwise similarities, output pairwise alignments:
vsearch --usearch_global queries.fas --db references.fas --id 0.8 --iddef 1 --alnout results.aln
Search a sequence dataset against itself (ignore self hits), get all matches with at least 60%
similarity, and collect results in a blast-like tab-separated format. Accept an unlimited number of hits
(--maxaccepts 0), and compare each query to all other sequences, including unlikely candidates
(--maxrejects 0):
vsearch --usearch_global queries.fas --db queries.fas --self --id 0.6 --blast6out results.blast6
--maxaccepts 0 --maxrejects 0
Shuffle the input fasta file (change the order of sequences) in a repeatable fashion (fixed seed), and
write unwrapped fasta sequences to the output file:
vsearch --shuffle queries.fas --output queries_shuffled.fas --randseed 13 --fasta_width 0
Sort by decreasing abundance the sequences contained in queries.fas (using the 'size=integer'
information), relabel the sequences while preserving the abundance information (with --sizeout), keep
only sequences with an abundance equal to or greater than 2:
vsearch --sortbysize queries.fas --output queries_sorted.fas --relabel sampleA_ --sizeout
--minsize 2
AUTHORS
Implementation by Torbjørn Rognes and Tomás Flouri, documentation by Frédéric Mahé.
CITATION
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016) VSEARCH: a versatile open source tool for
metagenomics. PeerJ 4:e2584 doi: 10.7717/peerj.2584 (link) ⟨https://doi.org/10.7717/peerj.2584⟩
REPORTING BUGS
Submit suggestions and bug-reports at (link) ⟨https://github.com/torognes/vsearch/issues⟩
<https://github.com/torognes/vsearch/issues>, send a pull request on (link) ⟨https://github.com/torognes/
vsearch⟩ <https://github.com/torognes/vsearch>, or compose a friendly or curmudgeont e-mail to Torbjørn
Rognes (link) ⟨torognes@ifi.uio.no⟩ <torognes@ifi.uio.no>.
AVAILABILITY
Source code and binaries are available at <https://github.com/torognes/vsearch>.
COPYRIGHT
Copyright (C) 2014-2024, Torbjørn Rognes, Frédéric Mahé and Tomás Flouri
All rights reserved.
Contact: Torbjørn Rognes <torognes@ifi.uio.no>, Department of Informatics, University of Oslo, PO Box
1080 Blindern, NO-0316 Oslo, Norway
This software is dual-licensed and available under a choice of one of two licenses, either under the
terms of the GNU General Public License version 3 or the BSD 2-Clause License.
GNU General Public License version 3
This program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see
(link) ⟨https://www.gnu.org/licenses/⟩ <https://www.gnu.org/licenses/>.
The BSD 2-Clause License
Redistribution and use in source and binary forms, with or without modification, are permitted provided
that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the
following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and
the following disclaimer in the documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
We would like to thank the authors of the following projects for making their source code available:
- vsearch includes code from Google's CityHash project by Geoff Pike and Jyrki Alakuijala,
providing some excellent hash functions available under a MIT license.
- vsearch includes code derived from Tatusov and Lipman's DUST program that is in the public
domain.
- vsearch includes public domain code written by Alexander Peslyak for the MD5 message digest
algorithm.
- vsearch includes public domain code written by Steve Reid and others for the SHA1 message digest
algorithm.
- vsearch binaries may include code from the zlib library, copyright Jean-Loup Gailly and Mark
Adler.
- vsearch binaries may include code from the bzip2 library, copyright Julian R. Seward.
SEE ALSO
swipe, an extremely fast pairwise local (Smith-Waterman) database search tool by Torbjørn Rognes,
available at (link) ⟨https://github.com/torognes/swipe⟩ <https://github.com/torognes/swipe>.
swarm, a fast and accurate amplicon clustering method by Frédéric Mahé and Torbjørn Rognes, available at
(link) ⟨https://github.com/torognes/swarm⟩ <https://github.com/torognes/swarm>.
VERSION HISTORY
New features and important modifications of vsearch (short lived or minor bug releases may not be
mentioned):
v1.0.0 released November 28th, 2014
First public release.
v1.0.1 released December 1st, 2014
Bug fixes (sortbysize, semicolon after size annotation in headers) and minor changes (labels as
secondary sort key for most sorts, treat T and U as identical for dereplication, only output size
in --dbmatched file if --sizeout specified).
v1.0.2 released December 6th, 2014
Bug fixes (ssse3/sse4.1 requirement, memory leak).
v1.0.3 released December 6th, 2014
Bug fix (now writes help to stdout instead of stderr).
v1.0.4 released December 8th, 2014
Added --allpairs_global option. Reduce memory requirements slightly and eliminate memory leaks.
v1.0.5 released December 9th, 2014
Fixes a minor bug with --allpairs_global and --acceptall options.
v1.0.6 released December 14th, 2014
Fixes a memory allocation bug in chimera detection (--uchime_ref option).
v1.0.7 released December 19th, 2014
Fixes a bug in the output from chimera detection with the --uchimeout option.
v1.0.8 released January 22nd, 2015
Introduces several changes and bug fixes:
- a new linear memory aligner for alignment of sequences longer than 5,000 nucleotides,
- a new --cluster_size command that sorts sequences by decreasing abundance before clustering,
- meaning of userfields qlo, qhi, tlo, thi changed for compatibility with usearch,
- new userfields qilo, qihi, tilo, tihi give alignment coordinates ignoring terminal gaps,
- in --uc output files, a perfect alignment is indicated with a '=' sign,
- the option --cluster_fast now sorts sequences by decreasing length, then by decreasing abundance
and finally by sequence identifier,
- default --maxseqlength value set to 50,000 nucleotides,
- fix for bug in alignment in rare cases,
- fix for lack of detection of under- or overflow in SIMD aligner.
v1.0.9 released January 22nd, 2015
Fixes a bug in the function sorting sequences by decreasing abundance (--sortbysize).
v1.0.10 released January 23rd, 2015
Fixes a bug where the --sizein option was ignored and always treated as on, affecting clustering
and dereplication commands.
v1.0.11 released February 5th, 2015
Introduces the possibility to output results in SAM format (for clustering, pairwise alignment and
searching).
v1.0.12 released February 6th, 2015
Temporarily fixes a problem with long headers in FASTA files.
v1.0.13 released February 17th, 2015
Fix a memory allocation problem when computing multiple sequence alignments with the --msaout and
--consout options, as well as a memory leak. Also increased line buffer for reading FASTA files
to 4MB.
v1.0.14 released February 17th, 2015
Fix a bug where the multiple alignment and consensus sequence computed after clustering ignored
the strand of the sequences. Also decreased size of line buffer for reading FASTA files to 1MB
again due to excessive stack memory usage.
v1.0.15 released February 18th, 2015
Fix bug in calculation of identity metric between sequences when using the MBL definition (--iddef
3).
v1.0.16 released February 19th, 2015
Integrated patches from Debian for increased compatibility with various architectures.
v1.1.0 released February 20th, 2015
Added the --quiet option to suppress all output to stdout and stderr except for warnings and fatal
errors. Added the --log option to write messages to a log file.
v1.1.1 released February 20th, 2015
Added info about --log and --quiet options to help text.
v1.1.2 released March 18th, 2015
Fix bug with large datasets. Fix format of help info.
v1.1.3 released March 18th, 2015
Fix more bugs with large datasets.
v1.2.0-1.2.19 released July 6th to September 8th, 2015
Several new commands and options added. Bugs fixed. Documentation updated.
v1.3.0 released September 9th, 2015
Changed to autotools build system.
v1.3.1 released September 14th, 2015
Several new commands and options. Bug fixes.
v1.3.2 released September 15th, 2015
Fixed memory leaks. Added '-h' shortcut for help. Removed extra 'v' in version number.
v1.3.3 released September 15th, 2015
Fixed bug in hexadecimal digits of MD5 and SHA1 digests. Added --samheader option.
v1.3.4 released September 16th, 2015
Fixed compilation problems with zlib and bzip2lib.
v1.3.5 released September 17th, 2015
Minor configuration/makefile changes to compile to native CPU and simplify makefile.
v1.4.0 released September 25th, 2015
Added --sizeorder option.
v1.4.1 released September 29th, 2015
Inserted public domain MD5 and SHA1 code to eliminate dependency on crypto and openssl libraries
and their licensing issues.
v1.4.2 released October 2nd, 2015
Dynamic loading of libraries for reading gzip and bzip2 compressed files if available.
Circumvention of missing gzoffset function in zlib 1.2.3 and earlier.
v1.4.3 released October 3rd, 2015
Fix a bug with determining amount of memory on some versions of Apple OS X.
v1.4.4 released October 3rd, 2015
Remove debug message.
v1.4.5 released October 6th, 2015
Fix memory allocation bug when reading long FASTA sequences.
v1.4.6 released October 6th, 2015
Fix subtle bug in SIMD alignment code that reduced accuracy.
v1.4.7 released October 7th, 2015
Fixes a problem with searching for or clustering sequences with repeats. In this new version,
vsearch looks at all words occurring at least once in the sequences in the initial step.
Previously only words occurring exactly once were considered. In addition, vsearch now requires at
least 10 words to be shared by the sequences, previously only 6 were required. If the query
contains less than 10 words, all words must be present for a match. This change seems to lead to
slightly reduced recall, but somewhat increased precision, ending up with slightly improved
overall accuracy.
v1.5.0 released October 7th, 2015
This version introduces the new option --minwordmatches that allows the user to specify the
minimum number of matching unique words before a sequence is considered further. New default
values for different word lengths are also set. The minimum word length is increased to 7.
v1.6.0 released October 9th, 2015
This version adds the relabeling options (--relabel, --relabel_md5 and --relabel_sha1) to the
shuffle command. It also adds the --xsize option to the clustering, dereplication, shuffling and
sorting commands.
v1.6.1 released October 14th, 2015
Fix bugs and update manual and help text regarding relabelling. Add all relabelling options to the
subsampling command. Add the --xsize option to chimera detection, dereplication and fastq
filtering commands. Refactoring of code.
v1.7.0 released October 14th, 2015
Add --relabel_keep option.
v1.8.0 released October 19th, 2015
Added --search_exact, --fastx_mask and --fastq_convert commands. Changed most commands to read
FASTQ input files as well as FASTA files. Modified --fastx_revcomp and --fastx_subsample to write
FASTQ files.
v1.8.1 released November 2nd, 2015
Fixes for compatibility with QIIME and older OS X versions.
v1.9.0 released November 12th, 2015
Added the --fastq_mergepairs command and associated options. This command has not been tested well
yet. Included additional files to avoid dependency of autoconf for compilation. Fixed an error
where identifiers in fasta headers where not truncated at tabs, just spaces. Fixed a bug in
detection of the file format (FASTA/FASTQ) of a gzip compressed input file.
v1.9.1 released November 13th, 2015
Fixed memory leak and a bug in score computation in --fastq_mergepairs, and improved speed.
v1.9.2 released November 17th, 2015
Fixed a bug in the computation of some values with --fastq_stats.
v1.9.3 released November 19th, 2015
Workaround for missing x86intrin.h with old compilers.
v1.9.4 released December 3rd, 2015
Fixed incrementation of counter when relabeling dereplicated sequences.
v1.9.5 released December 3rd, 2015
Fixed bug resulting in inferior chimera detection performance.
v1.9.6 released January 8th, 2016
Fixed bug in aligned sequences produced with --fastapairs and --userout (qrow, trow) options.
v1.9.7 released January 12th, 2016
Masking behaviour is changed somewhat to keep the letter case of the input sequences unchanged
when no masking is performed. Masking is now performed also during chimera detection.
Documentation updated.
v1.9.8 released January 22nd, 2016
Fixed bug causing segfault when chimera detection is performed on extremely short sequences.
v1.9.9 released January 22nd, 2016
Adjusted default minimum number of word matches during searches for improved performance.
v1.9.10 released January 25th, 2016
Fixed bug related to masking and lower case database sequences.
v1.10.0 released February 11th, 2016
Parallelized and improved merging of paired-end reads and adjusted some defaults. Removed progress
indicator when stderr is not a terminal. Added --fasta_score option to report chimera scores in
FASTA files. Added --rereplicate and --fastq_eestats commands. Fixed typos. Added relabelling to
files produced with --consout and --profile options.
v1.10.1 released February 23rd, 2016
Fixed a bug affecting the --fastq_mergepairs command causing FASTQ headers to be truncated at
first space (despite the bug fix release 1.9.0 of November 12th, 2015). Full headers are now
included in the output (no matter if --notrunclabels is in effect or not).
v1.10.2 released March 18th, 2016
Fixed a bug causing a segmentation fault when running --usearch_global with an empty query
sequence. Also fixed a bug causing imperfect alignments to be reported with an alignment string of
'=' in uc output files. Fixed typos in man file. Fixed fasta/fastq processing code regarding
presence or absence of compression library header files.
v1.11.1 released April 13th, 2016
Added strand information in UC file for --derep_fulllength and --derep_prefix. Added expected
errors (ee) to header of FASTA files specified with --fastaout and --fastaout_discarded when
--eeout or --fastq_eeout option is in effect for fastq_filter and fastq_mergepairs. The options
--eeout and --fastq_eeout are now equivalent.
v1.11.2 released June 21st, 2016
Two bugs were fixed. The first issue was related to the --query_cov option that used a different
coverage definition than the qcov userfield. The coverage is now defined as the fraction of the
whole query sequence length that is aligned with matching or mismatching residues in the target.
All gaps are ignored. The other issue was related to the consensus sequences produced during
clustering when only N's were present in some positions. Previously these would be converted to
A's in the consensus. The behaviour is changed so that N's are produced in the consensus, and it
should now be more compatible with usearch.
v2.0.0 released June 24th, 2016
This major new version supports reading from pipes. Two new options are added: --gzip_decompress
and --bzip2_decompress. One of these options must be specified if reading compressed input from a
pipe, but are not required when reading from ordinary files. The vsearch header that was
previously written to stdout is now written to stderr. This enables piping of results for further
processing. The file name '-' now represent standard input (/dev/stdin) or standard output
(/dev/stdout) when reading or writing files, respectively. Code for reading FASTA and FASTQ files
has been refactored.
v2.0.1 released June 30th, 2016
Avoid segmentation fault when masking very long sequences.
v2.0.2 released July 5th, 2016
Avoid warnings when compiling with GCC 6.
v2.0.3 released August 2nd, 2016
Fixed bad compiler options resulting in Illegal instruction errors when running precompiled
binaries.
v2.0.4 released September 1st, 2016
Improved error message for bad FASTQ quality values. Improved manual.
v2.0.5 released September 9th, 2016
Add options --fastaout_discarded and --fastqout_discarded to output discarded sequences from
subsampling to separate files. Updated manual.
v2.1.0 released September 16th, 2016
New command: --fastx_filter. New options: --fastq_maxlen, --fastq_truncee. Allow --minwordmatches
down to 3.
v2.1.1 released September 23rd, 2016
Fixed bugs in output to UC-files. Improved help text and manual.
v2.1.2 released September 28th, 2016
Fixed incorrect abundance output from fastx_filter and fastq_filter when relabelling.
v2.2.0 released October 7th, 2016
Added OTU table generation options --biomout, --mothur_shared_out and --otutabout to the
clustering and searching commands.
v2.3.0 released October 10th, 2016
Allowed zero-length sequences in FASTA and FASTQ files. Added --fastq_trunclen_keep option. Fixed
bug with output of OTU tables to pipes.
v2.3.1 released November 16th, 2016
Fixed bug where --minwordmatches 0 was interpreted as the default minimum word matches for the
given word length instead of zero. When used in combination with --maxaccepts 0 and --maxrejects 0
it will allow complete bypass of kmer-based heuristics.
v2.3.2 released November 18th, 2016
Fixed bug where vsearch reported the ordinal number of the target sequence instead of the cluster
number in column 2 on H-lines in the uc output file after clustering. For search and alignment
commands both usearch and vsearch reports the target sequence number here.
v2.3.3 released December 5th, 2016
A minor speed improvement.
v2.3.4 released December 9th, 2016
Fixed bug in output of sequence profiles and updated documentation.
v2.4.0 released February 8th, 2017
Added support for Linux on Power8 systems (ppc64le) and Windows on x86_64. Improved detection of
pipes when reading FASTA and FASTQ files. Corrected option for specifying output from
fastq_eestats command in help text.
v2.4.1 released March 1st, 2017
Fixed an overflow bug in fastq_stats and fastq_eestats affecting analysis of very large FASTQ
files. Fixed maximum memory usage reporting on Windows.
v2.4.2 released March 10th, 2017
Default value for fastq_minovlen increased to 16 in accordance with help text and for
compatibility with usearch. Minor changes for improved accuracy of paired-end read merging.
v2.4.3 released April 6th, 2017
Fixed bug with progress bar for shuffling. Fixed missing N-lines in UC files with usearch_global,
search_exact and allpairs_global when the output_no_hits option was not specified.
v2.4.4 released August 28th, 2017
Fixed a few minor bugs, improved error messages and updated documentation.
v2.5.0 released October 5th, 2017
Support for UDB database files. New commands: fastq_stripright, fastq_eestats2, makeudb_usearch,
udb2fasta, udbinfo, and udbstats. New general option: no_progress. New options minsize and maxsize
to fastx_filter. Minor bug fixes, error message improvements and documentation updates.
v2.5.1 released October 25th, 2017
Fixed bug with bad default value of 1 instead of 32 for minseqlength when using the
makeudb_usearch command.
v2.5.2 released October 30th, 2017
Fixed bug with where '-' as an argument to the fastq_eestats2 option was treated literally instead
of equivalent to stdin.
v2.6.0 released November 10th, 2017
Rewritten paired-end reads merger with improved accuracy. Decreased default value for
fastq_minovlen option from 16 to 10. The default value for the fastq_maxdiffs option is increased
from 5 to 10. There are now other more important restrictions that will avoid merging reads that
cannot be reliably aligned.
v2.6.1 released December 8th, 2017
Improved parallelisation of paired end reads merging.
v2.6.2 released December 18th, 2017
Fixed option xsize that was partially inactive for commands uchime_denovo, uchime_ref, and
fastx_filter.
v2.7.0 released February 13th, 2018
Added commands cluster_unoise, uchime2_denovo and uchime3_denovo contributed by Davide Albanese
based on Robert Edgar's papers. Refactored fasta and fastq print functions as well as code for
extraction of abundance and other attributes from the headers.
v2.7.1 released February 16th, 2018
Fix several bugs on Windows related to large files, use of "-" as a file name to mean stdin or
stdout, alignment errors, missed kmers and corrupted UDB files. Added documentation of UDB-related
commands.
v2.7.2 released April 20th, 2018
Added the sintax command for taxonomic classification. Fixed a bug with incorrect FASTA headers of
consensus sequences after clustering.
v2.8.0 released April 24th, 2018
Added the fastq_maxdiffpct option to the fastq_mergepairs command.
v2.8.1 released June 22nd, 2018
Fixes for compilation warnings with GCC 8.
v2.8.2 released August 21st, 2018
Fix for wrong placement of semicolons in header lines in some cases when using the sizeout or
xsize options. Reduced memory requirements for full-length dereplication in cases with many
duplicate sequences. Improved wording of fastq_mergepairs report. Updated manual regarding use of
sizein and sizeout with dereplication. Changed a compiler option.
v2.8.3 released August 31st, 2018
Fix for segmentation fault for --derep_fulllength with --uc.
v2.8.4 released September 3rd, 2018
Further reduce memory requirements for dereplication when not using the uc option. Fix output
during subsampling when quiet or log options are in effect.
v2.8.5 released September 26th, 2018
Fixed a bug in fastq_eestats2 that caused the values for large lengths to be much too high when
the input sequences had varying lengths.
v2.8.6 released October 9th, 2018
Fixed a bug introduced in version 2.8.2 that caused derep_fulllength to include the full FASTA
header in its output instead of stopping at the first space (unless the notrunclabels option is in
effect).
v2.9.0 released October 10th, 2018
Added the fastq_join command.
v2.9.1 released October 29th, 2018
Changed compiler options that select the target cpu and tuning to allow the software to run on any
64-bit x86 system, while tuning for more modern variants. Avoid illegal instruction error on some
architectures. Update documentation of rereplicate command.
v2.10.0 released December 6th, 2018
Added the sff_convert command to convert SFF files to FASTQ. Added some additional option argument
checks. Fixed segmentation fault bug after some fatal errors when a log file was specified.
v2.10.1 released December 7th, 2018
Improved sff_convert command. It will now read several variants of the SFF format. It is also able
to read from a pipe. Warnings are given if there are minor problems. Errors messages have been
improved. Minor speed and memory usage improvements.
v2.10.2 released December 10th, 2018
Fixed bug in sintax with reversed order of domain and kingdom.
v2.10.3 released December 19th, 2018
Ported to Linux on ARMv8 (aarch64). Fixed compilation warning with gcc version 8.1.0 and 8.2.0.
v2.10.4 released January 4th, 2019
Fixed serious bug in x86_64 SIMD alignment code introduced in version 2.10.3. Added link to
BioConda in README. Fixed bug in fastq_stats with sequence length 1. Fixed use of equals symbol in
UC files for identical sequences with cluster_fast.
v2.11.0 released February 13th, 2019
Added ability to trim and filter paired-end reads using the reverse option with the fastx_filter
and fastq_filter commands. Added --xee option to remove ee attributes from FASTA headers. Minor
invisible improvement to the progress indicator.
v2.11.1 released February 28th, 2019
Minor change to the handling of the weak_id and id options when using cluster_unoise.
v2.12.0 released March 19th, 2019
Take sequence abundance into account when computing consensus sequences or profiles after
clustering. Warn when rereplicating sequences without abundance info. Guess offset 33 in more
cases with fastq_chars. Stricter checking of option arguments and option combinations.
v2.13.0 released April 11th, 2019
Added the --fastx_getseq, --fastx_getseqs and --fastx_getsubseq commands to extract sequences from
a FASTA or FASTQ file based on their labels. Improved handling of ambiguous nucleotide symbols.
Corrected behaviour of --uchime_ref command with and options --self and --selfid. Strict detection
of illegal options for each command.
v2.13.1 released April 26th, 2019
Minor changes to the allowed options for each command. All commands now allow the log, quiet and
threads options. If more than 1 thread is specified for commands that are not multi-threaded, a
warning will be issued. Minor changes to the manual.
v2.13.2 released April 30th, 2019
Fixed bug related to improper handling of newlines on Windows. Allowed option strand plus to
uchime_ref for compatibility.
v2.13.3 released April 30th, 2019
Fixed bug in FASTQ parsing introduced in version 2.13.2.
v2.13.4 released May 10th, 2019
Added information about support for gzip- and bzip2-compressed input files to the output of the
version command. Adapted source code for compilation on FreeBSD and NetBSD systems.
v2.13.5 released July 2nd, 2019
Added cut command to fragment sequences at restriction sites. Silenced output from the fastq_stats
command if quiet option was given. Updated manual.
v2.13.6 released July 2nd, 2019
Added info about cut command to output of help command.
v2.13.7 released September 2nd, 2019
Fixed bug in consensus sequence introduced in version 2.13.0.
v2.14.0 released September 11th, 2019
Added relabel_self option. Made fasta_width, sizein, sizeout and relabelling options valid for
certain commands.
v2.14.1 released September 18th, 2019
Fixed bug with sequences written to file specified with fastaout_rev for commands fastx_filter and
fastq_filter.
v2.14.2 released January 28th, 2020
Fixed some issues with the cut, fastx_revcomp, fastq_convert, fastq_mergepairs, and
makeudb_usearch commands. Updated manual.
v2.15.0 released June 19th, 2020
Update manual and documentation. Turn on notrunclabels option for sintax command by default.
Change maxhits 0 to mean unlimited hits, like the default. Allow non-ascii characters in headers,
with a warning. Sort centroids and uc too when clusterout_sort specified. Add cluster id to
centroids output when clusterout_id specified. Improve error messages when parsing FASTQ files.
Add missing fastq_qminout option and fix label_suffix option for fastq_mergepairs. Add derep_id
command that dereplicates based on both label and sequence. Remove compilation warnings.
v2.15.1 released October 28th, 2020
Fix for dereplication when including reverse complement sequences and headers. Make some extra
checks when loading compression libraries and add more diagnostic output about them to the output
of the version command. Report an error when fastx_filter is used with FASTA input and options
that require FASTQ input. Update manual.
v2.15.2 released January 26th, 2021
No real functional changes, but some code and compilation changes. Compiles successfully on macOS
running on Apple Silicon (ARMv8). Binaries available. Code updated for C++11. Minor adaptations
for Windows compatibility, including the use of the C++ standard library for regular expressions.
Minor changes for compatibility with Power8. Switch to C++ header files.
v2.16.0 released March 22nd, 2021
This version adds the orient command. It also handles empty input files properly. Documentation
has been updated.
v2.17.0 released March 29nd, 2021
The fastq_mergepairs command has been changed. It now allows merging of sequences with overlaps as
short as 5 bp if the --fastq_minovlen option has been adjusted down from the default 10. In
addition, much fewer pairs of reads should now be rejected with the reason 'multiple potential
alignments' as the algorithm for detecting those have been changed.
v2.17.1 released June 14th, 2021
Modernized code. Minor changes to help info.
v2.18.0 released August 27th, 2021
Added the fasta2fastq command. Fixed search bug on ppc64le. Fixed bug with removal of size and ee
info in uc files. Fixed compilation errors in some cases. Made some general code improvements.
Updated manual.
v2.19.0 released December 21st, 2021
Added the lcaout and lca_cutoff options to enable the output of last common ancestor (LCA)
information about hits when searching. The randseed option was added as a valid option to the
sintax command. Code improvements.
v2.20.0 released January 10th, 2022
Added the fastx_uniques command and the fastq_qout_max option for dereplication of FASTQ files.
Some code cleaning.
v2.20.1 released January 11th, 2022
Fixes a bug in fastq_mergepair that caused an occational hang at the end when using multiple
threads.
v2.21.0 released January 12th, 2022
This version adds the sample, qsegout and tsegout options. It enables the use of UDB databases
with uchime_ref.
v2.21.1 released January 18th, 2022
Fix a problem with dereplication of empty input files. Update Altivec code on ppc64le for improved
compiler compatibility (vector->__vector).
v2.21.2 released September 12th, 2022
Fix problems with the lcaout option when using maxaccepts above 1 and either lca_cutoff below 1 or
with top_hits_only enabled. Update documentation. Update code to avoid compiler warnings.
v2.22.0 released September 19th, 2022
Add the derep_smallmem command for dereplication using little memory.
v2.22.1 released September 19th, 2022
Fix compiler warning.
v2.23.0 released July 7th, 2023
Update documentation. Add citation file. Modernize and improve code. Fix several minor bugs. Fix
compilation with GCC 13. Print stats after fastq_mergepairs to log file instead of stderr. Handle
sizein option correctly with dbmatched option for usearch_global. Allow maxseqlength option for
makeudb_usearch. Fix memory allocation problem with chimera detection. Add lengthout and xlength
options. Increase precision for eeout option. Add warning about sintax algorithm, random seed and
multiple threads. Refactor chimera detection code. Add undocumented experimental
long_chimeras_denovo command. Fix segfault with clustering. Add more references.
v2.24.0 released October 26th, 2023
Update documentation. Improve code. Allow up to 20 parents for the undocumented and experimental
chimeras_denovo command. Fix compilation warnings for sha1.c. Compile for release (not debug) by
default.
v2.25.0 released November 10th, 2023
Allow a given percentage of mismatches between chimeras and parents for the experimental
chimeras_denovo command.
v2.26.0 released November 24th, 2023
Enable the maxseqlength and minseqlength options for the chimera detection commands. When the
usearch_global or search_exact commands are used, OTU tables will include samples and OTUs with no
matches.
v2.26.1 released November 25th, 2023
No real changes, but the previous version was released without proper updates to the source code.
v2.27.0 released January 19th, 2024
The usearch_global and search_exact commands now support FASTQ files as well as FASTA files as
input. This version of vsearch includes clarifications and updates to the manual. Some code has
been refactored. Generic Dockerfiles for major Linux distributions have been included. Some
warnings from compilers and other tools have been eliminated. The release for Windows will also
include DLL's for the two compression libraries.
version 2.27.0 January 19, 2024 vsearch(1)