Difference between revisions of "HPC:bwa"
From HPC wiki
(Created page with "=== bwa === bwa 0.5.9-r16 is installed across all HPC nodes. ==== Usage ==== bwa can be called without the need for an environment module on any of the compute nodes. <pre> ...") |
|||
| (One intermediate revision by one other user not shown) | |||
| Line 3: | Line 3: | ||
==== Usage ==== | ==== Usage ==== | ||
| − | bwa can be called without the need for an environment module on any of the compute nodes. | + | At this time, bwa can be called without the need for an environment module on any of the compute nodes. |
<pre> | <pre> | ||
| Line 36: | Line 36: | ||
=== Other Pages === | === Other Pages === | ||
| + | ---- | ||
| + | <div class="mw-collapsible mw-collapsed"> | ||
| + | *[[HPC:FAQ|HPC FAQ ]] | ||
| + | *[[HPC:Login|Connecting to the PMACS cluster]] | ||
| + | *[[HPC:User_Guide|User Guide]] | ||
*[[HPC:Software|Available Software]] | *[[HPC:Software|Available Software]] | ||
| − | *[[HPC: | + | *[[HPC:Archive System|PMACS Archive System]] |
| − | + | </div> | |
| − | |||
Latest revision as of 15:27, 13 August 2019
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
