Difference between revisions of "Bismark"

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m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ")
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|bismark}}
 
|{{#vardefine:app|bismark}}
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|{{#vardefine:testing|}} <!--TESTING/PROFILING-->
 
|{{#vardefine:testing|}} <!--TESTING/PROFILING-->
 
|{{#vardefine:faq|}} <!--FAQ-->
 
|{{#vardefine:faq|}} <!--FAQ-->
|{{#vardefine:citation|}} <!--CITATION-->
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|{{#vardefine:citation|1}} <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|}
 
|}
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Bismark is a bisulfite read mapper and methylation caller.
 
Bismark is a bisulfite read mapper and methylation caller.
<!--Location-->
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
<!--Versions-->
 
==Available versions==
 
* 0.7.4 (EL6)
 
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Running the application using modules==
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==Environment Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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==System Variables==
 +
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Run-->
 
<!--Run-->
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{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
 
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
<!--Policy-->
 
<!--Policy-->
{{#if: {{#var: policy}}|==Usage policy==
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{{#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)
 
|}}
 
|}}
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{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
DOUBLE_CLICK_TO_WRITE_CITATION_HERE
+
 
 +
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for
 +
Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi:
 +
10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed
 +
Central PMCID: PMC3102221.
 
|}}
 
|}}
 
<!--Installation-->
 
<!--Installation-->

Latest revision as of 18:17, 12 August 2022

Description

bismark website  

Bismark is a bisulfite read mapper and methylation caller.

Environment Modules

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

System Variables

  • HPC_BISMARK_DIR - installation directory




Citation

If you publish research that uses bismark you have to cite it as follows:

Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed Central PMCID: PMC3102221.