Difference between revisions of "ALLPATHS-LG"
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#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== | ||
Revision as of 16:29, 10 August 2012
Description
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.
Execution Environment and 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