Is There Any Publicly Available Documentation About Velvet'S Source Code?

Question

[Tianyang Li]

Hi,

Is there any publicly available documentation about Velvet's source code? There are a few papers (Separating Metagenomic Short Reads into Genomes via Clustering, Efficient de novo assembly of single-cell bacterial genomes from short-read data sets) that used a modified Velvet, but I don't know how they got through Velvet's source code. Right now I'm interested in using parts of Velvet's source code, but I don't know how. Thanks for you help!

[Pierre Lindenbaum]

I'm afraid it's a self-documenting code :-)

[Lars Juhl Jensen]

"Self-documenting" meaning "we sure hope it documents itself, because nobody else does it" ;-)

[Science_Robot]

Are you sure they modified Velvet's source code and did not just pre-process reads?

Answer 1

[Pablacious]

You might want to take a look at Daniel Zerbino's PhD thesis at the EBI website:

http://www.ebi.ac.uk/training/ftp/PhDtheses/Daniel_Zerbino.pdf

I understand that Daniel is the main developer of Velvet.

[Bert Overduin]

He indeed is. Although he moved to UCSC I am pretty sure he is still happy to answer any questions regarding Velvet you may have. His email address is [e-mail].