Difference between revisions of "BWA"

Revision as of 21:01, 6 December 2019

Description

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.

Required Modules

modules documentation

Serial and Parallel

bwa

System Variables

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

@@ Line 1: / Line 1: @@
-__NOTOC__
+__NOTOC____NOEDITSECTION__
-__NOEDITSECTION__
+[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
-[[Category:Software]]
-<!-- ########  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-->
 |{{#vardefine:app|bwa}}
 |{{#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:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 31: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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}}}}
+==Required Modules==
-Available versions:
+[[Modules|modules documentation]]
-* 0.5.9
+===Serial and Parallel===
-* 0.5.10 (last 0.5 branch release)
+*{{#var:app}}
-* 0.6.0 (default, beware the changes that may be incompatible with 0.5 pipelines).
+==System Variables==
-<!-- -->
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-{{#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_MAN - manpage 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|}}
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 51: / Line 36: @@
 {{#if: {{#var: pbs}}|==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)|}}
 {{#if: {{#var: testing}}|==Performance==