Difference between revisions of "SOAPdenovo"
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Moskalenko (talk | contribs) m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "") |
Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
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* 1.05 - 31, 63 and 127 kmer versions are available as SOAPdenovo31mer, SOAPdenovo63mer and SOAPdenovo127mer | * 1.05 - 31, 63 and 127 kmer versions are available as SOAPdenovo31mer, SOAPdenovo63mer and SOAPdenovo127mer | ||
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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
* HPC_SOAPDENOVO_BIN - executable directory | * HPC_SOAPDENOVO_BIN - executable directory | ||
Revision as of 02:03, 10 August 2012
Description
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
Installed Versions
- 1.05 - 31, 63 and 127 kmer versions are available as SOAPdenovo31mer, SOAPdenovo63mer and SOAPdenovo127mer
Execution Environment and Modules
To use soapdenovo with the environment modules system at HPC the following commands are available:
Get module information for soapdenovo:
$module spider soapdenovo
Load the default application module:
$module load soapdenovo
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_SOAPDENOVO_DIR - directory where soapdenovo is located.
- HPC_SOAPDENOVO_BIN - executable directory