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.

Availability

Versions 1.2, 1.2.07, 1.2.09 and 1.2.10. Freely available to users. Modules:

velvet-1.2
velvet-1.2.07
velvet-1.2.09
velvet-1.2.10

VelvetOptimizer 2.2.5 is available too (module velvetopt-2.2.5).

Licence

GNU GPL3

Use

Initialize environment with command:

module add velvet-1.2.10-new

(or older version)

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

Program administrator

meta@cesnet.cz

Homepage

URL: http://www.ebi.ac.uk/~zerbino/velvet/ VelvetOptimiser: http://bioinformatics.net.au/software.velvetoptimiser.shtml