SOAPdenovo

Description

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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. Template:App Location

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