subread-align(1) an accurate and efficient aligner for mapping both genomic DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)


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.
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.
Convert color-space read bases to base-space read bases in the mapping output. Note that read mapping is performed at color-space.
Detect structural variants (eg. long indel, inversion, duplication and translocation) and report breakpoints. Refer to Users Guide for breakpoint reporting.
Input reads are in SAM format.
Input reads are in BAM format.
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
--DPGapExt <int>
Penalty for gap extension in short indel detection. 0 by default.
--DPMismatch <int> Penalty for mismatches in short indel detection. 0 by
--DPMatch <int>
Score for matched bases in short indel detection. 2 by default.
Detect multiple short indels that occur concurrently in a small genomic region (these indels could be as close as 1bp apart).
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.