xenial (1) subread-align.1.gz

Provided by: subread_1.5.0-p1+dfsg-2_amd64 bug

NAME

       subread-align  -  an  accurate  and  efficient aligner for mapping both genomic DNA-seq reads and RNA-seq
       reads (for the purpose of expression analysis)

USAGE

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

       Required arguments:

       -i <string>
              Base name of the index.

       -r <string>
              Name of the  input  file.  Input  formats  including  gzipped  fastq,  fastq,  and  fasta  can  be
              automatically detected. If paired-end, this should give the name of file including first reads.

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

       Optional arguments:

       -o <string>
              Name of the output file. By default, the output is in BAM format.

       -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. 3 by default

       -M <int>
              Specify the maximum  number  of  mis-matched  bases  allowed  in  the  alignment.  3  by  default.
              Mis-matches found in softclipped bases are not counted.

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

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

       -B <int>
              Maximal number of equally-best mapping locations to be reported. 1 by default. Note that -u option
              takes precedence over -B.

       -P <3:6>
              Format of Phred scores in input files, '3' for phred+33 and '6' for phred+64. '3' by default.

       -u     Report uniquely mapped reads only. Number of matched bases ( for RNA-seq) or mis-matched bases(for
              genomic DNA-seq) is used to break the tie.

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

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

       --SAMinput
              Input reads are in SAM format.

       --BAMinput
              Input reads are in BAM format.

       --SAMoutput
              Save mapping result in SAM format.

       --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.

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

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

       --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.

       --complexIndels
              Detect multiple short indels that occur concurrently in a small genomic region (these indels could
              be as close as 1bp apart).

       -v     Output version of the program.

       Optional arguments for paired-end reads:

       -R <string>
              Name of the file including second reads.

       -p <int>
              Consensus  threshold  for  the non-anchor read (receiving less votes than the anchor read from the
              same pair). 1 by default.

       -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).

       Refer to Users Manual for detailed description to the arguments.