Difference between revisions of "Cutadapt"

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m (Text replace - "==Available versions== (.*)+ <!-- -->" to "<!--Modules-->")
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
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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"
 
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{|
 
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|{{#vardefine:app|cutadapt}}
 
|{{#vardefine:app|cutadapt}}
 
|{{#vardefine:url|http://code.google.com/p/cutadapt/}}
 
|{{#vardefine:url|http://code.google.com/p/cutadapt/}}
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|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
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|{{#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 -->
 
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{{#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.
* HPC_CUTADAPT_BIN - executable directory
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
{{#if: {{#var: exe}}|==How To Run==
 
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{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
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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 18:44, 12 August 2022

Description

cutadapt website  

cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

Environment Modules

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

System Variables

  • HPC_CUTADAPT_DIR - installation directory