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