parallel de novo assembler

[tmy1018]

Hi,

I'm interested in using a parallel assembler for de novo assembler right now. I know that Abyss can use MPI and SOAPdenovo is multi-threaded. However, the machines available to me currently don't support MPI and SOAPdenovo is very hard to use without any useful docs. Can someone provide me with some more information on this topic? Thanks! :-)

[PatrickJ]

Sylvain Forêt and Daniel Zerbino are working on a parallel version of Velvet that should be available soon. Velvet works really well for de novo assembly, and if you are working with transcriptome data, try the multiple-k method (http://genome.cshlp.org/content/20/10/1432.full)

[bstamps]

Is there any more to this? I saw a publication recently showing an MPI adaptation to velvet, but the source was not published, and there is no mention of it on the Velvet website.

[rahularjun86]

Hi,
This could be of your interest http://seqanswers.com/forums/showthr...&highlight=Ray.
Thanks,
Rahul