Velvet

 

Velvet is a de novo sequence assembler for short reads produced by next-generation sequencing technology.

 

Documentation

 

Usage

 

  • Bridges

  • Greenfield

  • BioU

 

To see what versions of Velvet are available, type

module avail velvet

 

To see what Velvet commands are available and how to get additional help, type

module help velvet

 

Include the following command in your job script to enable Velvet

module load velvet

 

There are many versions of velvet available. Some are compiled with icc and some with gcc, and versions also differ in the maximum number of kmers that can be used. To see them all type

module avail velvet

 

You can see details on any version and how to get more help, including usage information for velveth and velvetg, by typing

module help specific-velvet-version

 

To run a velvet job, include a command like this in your batch script

module load specific-velvet-version

You may also have to load the module for icc or gcc; see the module help for details.

 

 

The Velvet programs are available through the Galaxy instance on biou.

To make the Velvet programs available through the command line, csh users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

To make the BEDTools programs available through the command line, bash users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE