SOAPdenovo2

Introduction

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. Now the new version is available. SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.

Installed version

The currently installed version of SOAPdenovo2 is r420.

Using SOAPdenovo2

If you want to find out more about SOAPdenovo2 on the HPC cluster, you can use the command

module spider SOAPdenovo2

This will show you basic informations e.g. a short description and the currently installed version.

To load the module, use the command

module load SOAPdenovo2

There is only one version of SOAPdenovo2 installed at the moment, if there should be more than one you would have to specify the right version to load:

module load SOAPdenovo2/r240

Always remember: this command is case sensitive!

Documentation

For further informations, please visit the official homepage.