Difference between revisions of "HPC:bwa"

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==== Usage ====
 
==== Usage ====
bwa can be called without the need for an environment module on any of the compute nodes.
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=== Other Pages ===
 
=== Other Pages ===
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----
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<div class="mw-collapsible mw-collapsed">
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*[[HPC:FAQ|HPC FAQ ]]
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*[[HPC:Login|Connecting to the PMACS cluster]]
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*[[HPC:User_Guide|User Guide]]
 
*[[HPC:Software|Available Software]]
 
*[[HPC:Software|Available Software]]
*[[HPC:User_Guide|User Guide]]
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*[[HPC:Archive System|PMACS Archive System]]
*[[HPC:Main_Page|HPC Main Page]]
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</div>
*[[HPC:Login|Connecting to the PMACS cluster]]
 

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

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