Velvet

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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

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of velvet and load default version of velvet as

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


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail velvet

and choose explicit version you want to use.

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

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