Difference between revisions of "ALLPATHS-LG"

From UFRC
Jump to navigation Jump to search
(Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...")
 
Line 41: Line 41:
 
==Available versions==
 
==Available versions==
 
* 39099 (Nov 2011)
 
* 39099 (Nov 2011)
 +
* 40122 (Jan 04, 2011)
 
<!-- -->
 
<!-- -->
 
{{#if: {{#var: mod}}|==Running the application using modules==
 
{{#if: {{#var: mod}}|==Running the application using modules==

Revision as of 20:54, 6 January 2012

Description

{{{name}}} website  
ALLPATHS-LG is a short read assembler. It has been designed to use reads produced by new sequencing technology machines such as the Illumina Genome Analyzer. This version has been optimized for, but not necessarily limited to, reads of length 100 bases. ALLPATHS is not designed to assemble Sanger or 454 FLX reads, or a mix of these with short reads. Template:App Location

Available versions

  • 39099 (Nov 2011)
  • 40122 (Jan 04, 2011)

Running the application using modules

To use allpathslg with the environment modules system at HPC the following commands are available:

Get module information for allpaths-lg:

$module spider allpathslg

Load the default application module:

$module load allpathslg

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_ALLPATHSLG_DIR - directory where allpathslg is located.
  • HPC_ALLPATHSLG_BIN - executable directory
  • HPC_ALLPATHSLG_DOC - documentation directory