Difference between revisions of "SOAPdenovo"
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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. | 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. | ||
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==Installed Versions== | ==Installed Versions== | ||
* 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 | ||
Revision as of 02:00, 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
Running the application using 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