Difference between revisions of "FAR"

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(Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:BioinformaticsCategory:Genomics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the v...")
 
 
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
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{|<!--Main settings - REQUIRED-->
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MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|far}}
 
|{{#vardefine:app|far}}
 
|{{#vardefine:url|http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page}}
 
|{{#vardefine:url|http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page}}
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<!--Description-->
 
<!--Description-->
 
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FAR is a software that removes adapter sequences from your sequencing reads by overlap alignment using the Needleman Wunsch algorithm (default) or a quality-based variant of the Needleman Wunsch algorithm. The Needleman Wunsch algorithm is a global exact string-matching algorithm, which offers maximal sensitivity and outperforms heuristic algorithm such as BLAST. Therefore the alignment of an adapter sequence to a read is very accurate.
 
FAR is a software that removes adapter sequences from your sequencing reads by overlap alignment using the Needleman Wunsch algorithm (default) or a quality-based variant of the Needleman Wunsch algorithm. The Needleman Wunsch algorithm is a global exact string-matching algorithm, which offers maximal sensitivity and outperforms heuristic algorithm such as BLAST. Therefore the alignment of an adapter sequence to a read is very accurate.
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Environment Modules==
==Available versions==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 2.15
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: mod}}|==Running the application using modules==
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* LD_LIBRARY_PATH - run time library path
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* LD_LIBRARY_PATH - executable directory
 
 
 
 
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{{#if: {{#var: conf}}|==Configuration==
 
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
{{#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.|}}
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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)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 18:54, 12 August 2022

Description

far website  

FAR is a software that removes adapter sequences from your sequencing reads by overlap alignment using the Needleman Wunsch algorithm (default) or a quality-based variant of the Needleman Wunsch algorithm. The Needleman Wunsch algorithm is a global exact string-matching algorithm, which offers maximal sensitivity and outperforms heuristic algorithm such as BLAST. Therefore the alignment of an adapter sequence to a read is very accurate.

Environment Modules

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

System Variables

  • HPC_FAR_DIR - installation directory
  • LD_LIBRARY_PATH - run time library path