Difference between revisions of "FAR"
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
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{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Revision as of 16:30, 10 August 2012
Description
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.
Execution Environment and Modules
To use far with the environment modules system at HPC the following commands are available:
Get module information for far:
$module spider far
Load the default application module:
$module load far
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_FAR_DIR - directory where far is located.
- LD_LIBRARY_PATH - run time library path