Big Genomes and Velvet

[azroger]

I was asked to get an estimate of how much memory it realistically takes to run Velvet to assemble a large genome, e.g. human genome size. If anybody had some idea or experience it would be a help. Even if you have experience with Velvet and a genome in the 100's of mb range, it could be helpful. I would guess roughly 20X coverage may be a reasonable size to consider, but it could take more to really assemble a genome successfully from small reads.

[spenthil]

This has been addressed a few times before:

http://seqanswers.com/forums/showthread.php?t=2101

http://www.google.com/search?sourceid=chrome&ie=UTF-8&q=Big+Genomes+and+Velvet#sclient=psy&hl=en&q=+site%3Aseqanswers.com+Big+Genomes+and+Velvet+memory&aq=f&aqi=&aql=&oq=&pbx=1&fp=27b7e57d321f7805

[Thorondor]

spenthil ist right, check first if there is already some information that helps you.

And there is an velvet mailing list, http://listserver.ebi.ac.uk/mailman/...o/velvet-users where zerbino is also very active.

The RAM you need depends a lot on the kmer (hash) you choose. Normally the higher your coverage and your minimum read length the higher kmer (hash) you can choose and therefore less RAM you will need. For a human genome depending on the quality of your reads you will still need around 64 - 128GB RAM.

[azroger]

Thanks very much for the help. I did check for previous answers, but I didn't find these. I'm pretty new at using SeqAnswers. I think your answers pretty well cover my question.