Difference between revisions of "Cutadapt"

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(Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:BioinformaticsCategory:NGS <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variab...")
 
 
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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-->
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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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<!--Description-->
 
<!--Description-->
 
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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.
 
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.
<!--Location-->
 
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
==Available versions==
 
* 1.0
 
  
''Note: cutadapt is installed into the python 2.6.5 and so the cutadapt module loads python/2.6.5''
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==Environment Modules==
{{#if: {{#var: mod}}|==Running the application using modules==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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==System Variables==
* HPC_CUTADAPT_BIN - executable directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
{{#if: {{#var: exe}}|==How To Run==
 
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{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#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