metaVelvet

Overview

metaVelvet provides an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.

Version 1.2.02 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v2 license and all use must adhere to that license.

Set up procedure

To access the software you must first load one of the modulefiles:

# Compiled with Intel compiler - app may run faster.
module load apps/intel-15.0/metavelvet/1.2.02

# Compiled with GCC compiler.
module load apps/gcc/metavelvet/1.2.02

Running the application

Please do not run metavelvet on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

meta-velvetg arg1 arg2 ...

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• MetaVelvet website

Updates

None.