[mira_talk] Re: Solexa de-novo assembly of paired reads
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 12 Jul 2010 20:45:11 +0200
On Montag 12 Juli 2010 Tony Travis wrote:
> I'm trying to assemble about 20,000,000 paired-end Solexa reads using
> MIRA V3.0.3 (production version). The job has been running for three
> weeks now but has not yet completed the first pass.
Umm ... you missed some announcements regarding the 3.1.15 development
version? There were some optimisations which make de-novo assembly of Solexa
much more bearable time-wise.
Please stop that process and use 3.2.0rc1. Should do wonders (days instead of
weeks).
> I don't know the fragment sizes for this run, but do you think that MIRA
> is taking so long because I didn't include the appropriate fragment sizes?
No, it's simply the "I need to assemble everything under the sun, and be it
just two Solexa reads a contig" syndrome of MIRA. As I said, should be much
better in 3.2.0rc1
B.
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