NAME

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

DESCRIPTION

       Version 2.0.1

       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 Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.