Velvet

Description

Velvet is frequently used assembler in many sequencing projects that are focused on de novo assembly from NGS technology data. Velvet is capable of handling paired and also single reads. It permits the user to set many of assembly conditions.

License

GNU GPL3

Usage

module avail velvet/ # list available modules
module load velvet   # load (default) module

Known problems

• If program Velvetg end with "core dumped", try to change the k-mer parameter to other value. Last time there was a problem with values 11 and 13. If you need work with short k-mers, use velvet version 1.2.09 which is compiled with parameter BIGASSEMBLY=1. It can be helpfull.

Documentation

Documentation is available at Velvet official website. https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf and https://github.com/dzerbino/velvet/wiki/Manual

Homepage

• Velvet: http://www.ebi.ac.uk/~zerbino/velvet/ and https://github.com/dzerbino/velvet
• VelvetOptimiser: http://bioinformatics.net.au/software.velvetoptimiser.shtml