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.