Difference between revisions of "FAR"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!--Compiler and MPI settings - OPTIONAL --> |{" to "|{")
 
(4 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+
[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|<!--Main settings - REQUIRED-->
 
{|<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|far}}
 
|{{#vardefine:app|far}}
Line 19: Line 19:
  
 
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.
 
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
[[Modules|modules documentation]]
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
+
==System Variables==
*{{#var:app}}
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* LD_LIBRARY_PATH - run time library path
 
* LD_LIBRARY_PATH - run time library path
 
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}

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