parallel de novo assembler

tmy1018 · 03-02-2011, 03:04 PM

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 · 03-02-2011, 09:44 PM

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 · 10-22-2012, 09:27 AM

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 · 10-22-2012, 09:31 AM

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

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03-02-2011, 03:04 PM	#1
tmy1018 Member Location: Beijing Join Date: Feb 2011 Posts: 10	parallel de novo assembler 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! :-)

10-22-2012, 09:31 AM	#4
rahularjun86 Member Location: Frankfurt(M), Germany Join Date: Jan 2011 Posts: 58	Hi, This could be of your interest http://seqanswers.com/forums/showthr...&highlight=Ray. Thanks, Rahul __________________ Rahul Sharma, Ph.D Frankfurt am Main, Germany

03-02-2011, 09:44 PM	#2
PatrickJ Junior Member Location: Ames, IA Join Date: Nov 2010 Posts: 2	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)

10-22-2012, 09:27 AM	#3
bstamps Member Location: University of Oklaoma Join Date: Oct 2012 Posts: 40	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.