BFAST: Difference between revisions

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__NOTOC__
__NOTOC__
__NOEDITSECTION__
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
[[Category:Software]][[Category:Biology]][[Category:NGS]]
<!-- ########  Template Configuration ######## -->
{|<!--Main settings - REQUIRED-->
<!--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|bfast}}
|{{#vardefine:app|bfast}}
|{{#vardefine:url|http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page}}
|{{#vardefine:url|http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page}}
<!--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-->
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BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.
BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.


==Available versions==
<!--Modules-->
* 0.7.0a
==Environment Modules==
<!-- -->
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
{{#if: {{#var: mod}}|==Running the application using modules==
==System Variables==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_BFAST_BIN - executable directory
* HPC_BFAST_BIN - executable directory
* HPC_BFAST_DOC - documentation directory
* HPC_BFAST_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==
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{{#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 18:16, 12 August 2022

Description

bfast website  

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.

Environment Modules

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

System Variables

  • HPC_BFAST_DIR - installation directory
  • HPC_BFAST_BIN - executable directory
  • HPC_BFAST_DOC - documentation directory




Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=BFAST&oldid=24727"