Difference between revisions of "Oases"
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
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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 16:32, 10 August 2012
Description
Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).
Execution Environment and Modules
To use oases with the environment modules system at HPC the following commands are available:
Get module information for oases:
$module spider oases
Load the default application module:
$module load oases
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_OASES_DIR - directory where oases is located.
- HPC_OASES_BIN
- HPC_OASES_DOC