Provided by: fastp_0.23.4+dfsg-1_amd64 
NAME
fastp - Ultra-fast all-in-one FASTQ preprocessor
DESCRIPTION
fastp: an ultra-fast all-in-one FASTQ preprocessor version 0.23.0 usage: fastp [options] ... options:
-i, --in1
read1 input file name (string [=])
-o, --out1
read1 output file name (string [=])
-I, --in2
read2 input file name (string [=])
-O, --out2
read2 output file name (string [=])
--unpaired1
for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to
discard it. (string [=])
--unpaired2
for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is
same as --unpaired1 (default mode), both unpaired reads will be written to this same file. (string
[=])
--overlapped_out
for each read pair, output the overlapped region if it has no any mismatched base. (string [=])
--failed_out
specify the file to store reads that cannot pass the filters. (string [=])
-m, --merge
for paired-end input, merge each pair of reads into a single read if they are overlapped. The
merged reads will be written to the file given by --merged_out, the unmerged reads will be written
to the files specified by --out1 and --out2. The merging mode is disabled by default.
--merged_out
in the merging mode, specify the file name to store merged output, or specify --stdout to stream
the merged output (string [=])
--include_unmerged
in the merging mode, write the unmerged or unpaired reads to the file specified by --merge.
Disabled by default.
-6, --phred64
indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will
still be phred33)
-z, --compression
compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4. (int [=4])
--stdin
input from STDIN. If the STDIN is interleaved paired-end FASTQ, please also add --interleaved_in.
--stdout
stream passing-filters reads to STDOUT. This option will result in interleaved FASTQ output for
paired-end output. Disabled by default.
--interleaved_in
indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by
default.
--reads_to_process
specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])
--dont_overwrite
don't overwrite existing files. Overwritting is allowed by default.
--fix_mgi_id
the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix
it.
-V, --verbose
output verbose log information (i.e. when every 1M reads are processed).
-A, --disable_adapter_trimming
adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
-a, --adapter_sequence
the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE
data, this is used if R1/R2 are found not overlapped. (string [=auto])
--adapter_sequence_r2
the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not
specified, it will be the same as <adapter_sequence> (string [=auto])
--adapter_fasta
specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file
(string [=])
--detect_adapter_for_pe
by default, the auto-detection for adapter is for SE data input only, turn on this option to
enable it for PE data.
-f, --trim_front1
trimming how many bases in front for read1, default is 0 (int [=0])
-t, --trim_tail1
trimming how many bases in tail for read1, default is 0 (int [=0])
-b, --max_len1
if read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1.
Default 0 means no limitation (int [=0])
-F, --trim_front2
trimming how many bases in front for read2. If it's not specified, it will follow read1's settings
(int [=0])
-T, --trim_tail2
trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings
(int [=0])
-B, --max_len2
if read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2.
Default 0 means no limitation. If it's not specified, it will follow read1's settings (int [=0])
-D, --dedup
enable deduplication to drop the duplicated reads/pairs
--dup_calc_accuracy
accuracy level to calculate duplication (1~6), higher level uses more memory (1G, 2G, 4G, 8G, 16G,
24G). Default 1 for no-dedup mode, and 3 for dedup mode. (int [=0])
--dont_eval_duplication
don't evaluate duplication rate to save time and use less memory.
-g, --trim_poly_g
force polyG tail trimming, by default trimming is automatically enabled for Illumina
NextSeq/NovaSeq data
--poly_g_min_len
the minimum length to detect polyG in the read tail. 10 by default. (int [=10])
-G, --disable_trim_poly_g
disable polyG tail trimming, by default trimming is automatically enabled for Illumina
NextSeq/NovaSeq data
-x, --trim_poly_x
enable polyX trimming in 3' ends.
--poly_x_min_len
the minimum length to detect polyX in the read tail. 10 by default. (int [=10])
-5, --cut_front
move a sliding window from front (5') to tail, drop the bases in the window if its mean quality <
threshold, stop otherwise.
-3, --cut_tail
move a sliding window from tail (3') to front, drop the bases in the window if its mean quality <
threshold, stop otherwise.
-r, --cut_right
move a sliding window from front to tail, if meet one window with mean quality < threshold, drop
the bases in the window and the right part, and then stop.
-W, --cut_window_size
the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4
(int [=4])
-M, --cut_mean_quality
the mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36
default: 20 (Q20) (int [=20])
--cut_front_window_size
the window size option of cut_front, default to cut_window_size if not specified (int [=4])
--cut_front_mean_quality
the mean quality requirement option for cut_front, default to cut_mean_quality if not specified
(int [=20])
--cut_tail_window_size
the window size option of cut_tail, default to cut_window_size if not specified (int [=4])
--cut_tail_mean_quality
the mean quality requirement option for cut_tail, default to cut_mean_quality if not specified
(int [=20])
--cut_right_window_size
the window size option of cut_right, default to cut_window_size if not specified (int [=4])
--cut_right_mean_quality
the mean quality requirement option for cut_right, default to cut_mean_quality if not specified
(int [=20])
-Q, --disable_quality_filtering
quality filtering is enabled by default. If this option is specified, quality filtering is
disabled
-q, --qualified_quality_phred
the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified.
(int [=15])
-u, --unqualified_percent_limit
how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
-n, --n_base_limit
if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5
(int [=5])
-e, --average_qual
if one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means
no requirement (int [=0])
-L, --disable_length_filtering
length filtering is enabled by default. If this option is specified, length filtering is disabled
-l, --length_required
reads shorter than length_required will be discarded, default is 15. (int [=15])
--length_limit
reads longer than length_limit will be discarded, default 0 means no limitation. (int [=0])
-y, --low_complexity_filter
enable low complexity filter. The complexity is defined as the percentage of base that is
different from its next base (base[i] != base[i+1]).
-Y, --complexity_threshold
the threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is
required. (int [=30])
--filter_by_index1
specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line
(string [=])
--filter_by_index2
specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line
(string [=])
--filter_by_index_threshold
the allowed difference of index barcode for index filtering, default 0 means completely identical.
(int [=0])
-c, --correction
enable base correction in overlapped regions (only for PE data), default is disabled
--overlap_len_require
the minimum length to detect overlapped region of PE reads. This will affect overlap analysis
based PE merge, adapter trimming and correction. 30 by default. (int [=30])
--overlap_diff_limit
the maximum number of mismatched bases to detect overlapped region of PE reads. This will affect
overlap analysis based PE merge, adapter trimming and correction. 5 by default. (int [=5])
--overlap_diff_percent_limit
the maximum percentage of mismatched bases to detect overlapped region of PE reads. This will
affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%.
(int [=20])
-U, --umi
enable unique molecular identifier (UMI) preprocessing
--umi_loc
specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none
(string [=])
--umi_len
if the UMI is in read1/read2, its length should be provided (int [=0])
--umi_prefix
if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG,
final=UMI_AATTCG). No prefix by default (string [=])
--umi_skip
if the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0 (int [=0])
-p, --overrepresentation_analysis
enable overrepresented sequence analysis.
-P, --overrepresentation_sampling
one in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis
(1~10000), smaller is slower, default is 20. (int [=20])
-j, --json
the json format report file name (string [=fastp.json])
-h, --html
the html format report file name (string [=fastp.html])
-R, --report_title
should be quoted with ' or ", default is "fastp report" (string [=fastp report])
-w, --thread
worker thread number, default is 3 (int [=3])
-s, --split
split output by limiting total split file number with this option (2~999), a sequential number
prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
-S, --split_by_lines
split output by limiting lines of each file with this option(>=1000), a sequential number prefix
will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0])
-d, --split_prefix_digits
the digits for the sequential number padding (1~10), default is 4, so the filename will be padded
as 0001.xxx, 0 to disable padding (int [=4])
--cut_by_quality5
DEPRECATED, use --cut_front instead.
--cut_by_quality3
DEPRECATED, use --cut_tail instead.
--cut_by_quality_aggressive
DEPRECATED, use --cut_right instead.
--discard_unmerged
DEPRECATED, no effect now, see the introduction for merging.
-?, --help
print this message
AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
fastp 0.23.0 October 2021 FASTP(1)