Difference between revisions of "HPC:bwa"
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Revision as of 15:54, 4 November 2014
bwa
bwa 0.5.9-r16 is installed across all HPC nodes.
Usage
At this time, bwa can be called without the need for an environment module on any of the compute nodes.
[asrini@consign ~]$ bsub -Is bash
[asrini@node061 ~]$ bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.5.9-r16
Contact: Heng Li <lh3@sanger.ac.uk>
Usage: bwa <command> [options]
Command: index index sequences in the FASTA format
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
pac_rev generate reverse PAC
bwt2sa generate SA from BWT and Occ
pac2cspac convert PAC to color-space PAC
stdsw standard SW/NW alignment
