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

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!

velvet code
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updated by Pablacious Pablacious • written by Tianyang Li • Tianyang Li

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

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written by Lars Juhl Jensen Lars Juhl Jensen

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

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written by Science_Robot Science_Robot

1 answer

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.

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written by Pablacious Pablacious

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 dzerbino@soe.ucsc.edu.

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written by Bert Overduin Bert Overduin

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