Velvet

 

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

 

Documentation

 

Usage

 

  • Bridges

  • BioU

 

There are many versions of velvet available. Versions differ in the maximum number of kmers that can be used. To see what versions of Velvet are available, 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

Include the following command in your job script to enable Velvet

module load specific-velvet-version

 

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

 

User Information

Passwords
Connect to PSC systems:
Policies
Technical questions:

Send mail to remarks@psc.edu or call the PSC hotline: 412-268-6350.