Difference between revisions of "BWA"

From UFRC
Jump to navigation Jump to search
m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ")
 
(10 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]]
<!-- ########  Template Configuration ######## -->
 
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
 
{|
 
{|
 
<!--Main settings - REQUIRED-->
 
<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|bwa}}
 
|{{#vardefine:app|bwa}}
 
|{{#vardefine:url|http://bio-bwa.sourceforge.net/}}
 
|{{#vardefine:url|http://bio-bwa.sourceforge.net/}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
Line 33: Line 19:
  
 
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.  
 
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.  
<!--Location-->
+
<!--Modules-->
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+
==Environment Modules==
==Available versions==
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 0.5.9
+
==System Variables==
* 0.5.10 (last 0.5 branch release)
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* 0.6.0 (default, beware the changes that may be incompatible with 0.5 pipelines).
 
<!-- -->
 
{{#if: {{#var: mod}}|==Running the application using modules==
 
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
 
* HPC_BWA_BIN - executable directory
 
* HPC_BWA_BIN - executable directory
 
* HPC_BWA_MAN - manpage directory
 
* HPC_BWA_MAN - manpage directory
 
* HPC_BWA_DOC - documentation directory
 
* HPC_BWA_DOC - documentation directory
{{#if: {{#var: exe}}|==How To Run==
+
<!--Additional-->
 +
{{#if: {{#var: exe}}|==Additional Information==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 51: Line 34:
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
+
{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 18:22, 12 August 2022

Description

bwa website  

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.

Environment Modules

Run module spider bwa to find out what environment modules are available for this application.

System Variables

  • HPC_BWA_DIR - installation directory
  • HPC_BWA_BIN - executable directory
  • HPC_BWA_MAN - manpage directory
  • HPC_BWA_DOC - documentation directory