Revision as of 16:33, 10 August 2012 by Moskalenko (talk | contribs) (Text replace - "Usage policy" to "Usage Policy")
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soapdenovo website  

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