NAME

       subread-align - toolkit for processing next-gen sequencing data

DESCRIPTION

       Version 2.0.4

       Usage:

       ./subread-align [options] -i <index_name> -r <input> -t <type> -o <output>

       ## Mandatory arguments:

       -i <string>
              Base name of the index.

       -r <string>
              Name  of  an  input  read  file.  If  paired-end,  this  should  be the first read file (typically
              containing "R1"in the file name) and the second should be provided via "-R".   Acceptable  formats
              include   gzipped   FASTQ,   FASTQ,  gzipped  FASTA  and  FASTA.   These  formats  are  identified
              automatically.

       -t <int>
              Type of input sequencing data. Its values include 0: RNA-seq data 1: genomic DNA-seq data.

       ## Optional arguments: # input reads and output

       -o <string>
              Name of an output file. By default, the output is in BAM format. Omitting this  option  makes  the
              output be written to STDOUT.

       -R <string>
              Name of the second read file in paired-end data (typically containing "R2" the file name).

       --SAMinput
              Input reads are in SAM format.

       --BAMinput
              Input reads are in BAM format.

       --SAMoutput
              Save mapping results in SAM format.

       # Phred offset

       -P <3:6>
              Offset  value  added  to  the  Phred quality score of each read base. '3' for phred+33 and '6' for
              phred+64. '3' by default.

       # thresholds for mapping

       -n <int>
              Number of selected subreads, 10 by default.

       -m <int>
              Consensus threshold for reporting a hit (minimal number of subreads that map in  consensus)  .  If
              paired-end,  this  gives  the  consensus  threshold for the anchor read (anchor read receives more
              votes than the other read in the same pair).  3 by default

       -p <int>
              Consensus threshold for the non- anchor read in a pair. 1 by default.

       -M <int>
              Maximum number of mis-matched bases allowed in each reported alignment. 3 by default.  Mis-matched
              bases found in softclipped bases are not counted.

       # unique mapping and multi-mapping

       --multiMapping
              Report  multi-mapping  reads  in  addition  to  uniquely mapped reads. Use "-B" to set the maximum
              number of equally-best alignments to be reported.

       -B <int>
              Maximum number of equally-best alignments to be reported for a  multi-mapping  read.  Equally-best
              alignments have the same number of mis-matched bases. 1 by default.

       # indel detection

       -I <int>
              Maximum  length  (in  bp) of indels that can be detected. 5 by default. Indels of up to 200bp long
              can be detected.

       --complexIndels
              Detect multiple short indels that are in close proximity (they can be as close as 1bp  apart  from
              each other).

       # read trimming

       --trim5 <int>
              Trim off <int> number of bases from 5' end of each read. 0 by default.

       --trim3 <int>
              Trim off <int> number of bases from 3' end of each read. 0 by default.

       # distance and orientation of paired end reads

       -d <int>
              Minimum fragment/insert length, 50bp by default.

       -D <int>
              Maximum fragment/insert length, 600bp by default.

       -S <ff:fr:rf>
              Orientation of first and second reads, 'fr' by default ( forward/reverse).

       # number of CPU threads

       -T <int>
              Number of CPU threads used, 1 by default.

       # read group

       --rg-id <string>
              Add read group ID to the output.

       --rg <string>
              Add <tag:value> to the read group (RG) header in the output.

       # read order

       --keepReadOrder
              Keep order of reads in BAM output the same as that in the input file. Reads from the same pair are
              always placed next to each other no matter this option is specified or not.

       --sortReadsByCoordinates Output location-sorted reads. This option is
              applicable  for  BAM  output only. A BAI index file is also generated for each BAM file so the BAM
              files can be directly loaded into a genome browser.

       # color space reads

       -b     Convert color-space read bases to base-space read bases in the  mapping  output.  Note  that  read
              mapping is performed at color-space.

       # dynamic programming

       --DPGapOpen <int> Penalty for gap opening in short indel detection. -1 by
              default.

       --DPGapExt <int>
              Penalty for gap extension in short indel detection. 0 by default.

       --DPMismatch <int> Penalty for mismatches in short indel detection. 0 by
              default.

       --DPMatch <int>
              Score for matched bases in short indel detection. 2 by default.

       # detect structural variants

       --sv   Detect  structural  variants (eg. long indel, inversion, duplication and translocation) and report
              breakpoints. Refer to Users Guide for breakpoint reporting.

       # gene annotation

       -a     Name of an annotation file (gzipped file is accepted).  GTF/GFF format by default. See  -F  option
              for more format information.

       -F     Specify  format  of  the provided annotation file. Acceptable formats include 'GTF' (or compatible
              GFF format) and 'SAF'. 'GTF' by default. For SAF format, please refer to Users Guide.

       -A     Provide a chromosome name alias file to match chr names in annotation with  those  in  the  reads.
              This should be a twocolumn comma-delimited text file. Its first column should include chr names in
              the  annotation  and  its  second column should include chr names in the index. Chr names are case
              sensitive. No column header should be included in the file.

       --gtfFeature <string>
              Specify feature type in GTF annotation. 'exon' by default. Features used for read counting will be
              extracted from annotation using the provided value.

       --gtfAttr <string>
              Specify attribute type in GTF annotation.  'gene_id'  by  default.  Meta-features  used  for  read
              counting will be extracted from annotation using the provided value.

       # others

       -v     Output version of the program.

       Refer to Users Manual for detailed description to the arguments.

AUTHOR

        This manpage was written by Alexandre Mestiashvili for the Debian distribution and
        can be used for any other usage of the program.

subread-align 2.0.3                                March 2023                                   SUBREAD-ALIGN(1)