Difference between revisions of "Bamtools"

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__NOTOC__
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]]
<!-- ########  Template Configuration ######## -->
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{|<!--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|bamtools}}
 
|{{#vardefine:app|bamtools}}
 
|{{#vardefine:url|https://github.com/pezmaster31/bamtools/wiki}}
 
|{{#vardefine:url|https://github.com/pezmaster31/bamtools/wiki}}
<!--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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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
==Additional tools==
 
==Additional tools==
 
We also provide small tools that depend on bamtools or are built against it within this module.
 
We also provide small tools that depend on bamtools or are built against it within this module.

Latest revision as of 18:02, 12 August 2022

Description

bamtools website  

BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.

Environment Modules

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

System Variables

  • HPC_BAMTOOLS_DIR - installation directory

Additional tools

We also provide small tools that depend on bamtools or are built against it within this module.

  • bamaddrg (2012-01-27 build against bamtools 0.9.4).