Difference between revisions of "Bismark"

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m (Text replace - "Usage policy" to "Usage Policy")
 
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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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<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Execution Environment and 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==
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* 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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{{#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
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 +
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for
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Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi:
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10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed
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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.