Velvet
Velvet is a de novo sequence assembler for short reads produced by next-generation sequencing technology.
Documentation
- www.ncbi.nlm.nih.gov/pubmed/18349386
- www.ncbi.nlm.nih.gov/pmc/articles/PMC2952100/
- thegenomefactory.blogspot.com/2012/09/using-velvet-with-mate-pair-sequences.html
Usage on Bridges
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 or interactive session to enable Velvet
module load specific-velvet-version
Usage on BioU
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
