[mira_talk] Re: miramem under-estimate
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 23 Nov 2010 08:45:50 +0100
On Montag 22 November 2010 Laurent MANCHON wrote:
> Genome assembly is a big problem moreover when you have more and more
> reads, i just got a genome of 400 Mb finished and I can tell i was
> monitoring the RAM of the server for many weeks...
> I have used the latest ABYSS with 320 millions of reads.
> [...]
> I have tested Mira for Paired-end assembly and with million of reads
> mira is a beast that consumes a lot of RAM ...and has a bad memory
> footprint.
Yeah, there are a couple of things MIRA is not good at ... working with >20 to
40 million reads is one of them.
I think the future of (de-novo) sequencing will not stay with short reads.
Therefore I'll work on improving behaviour with ultra-high read numbers
gradually, but put my priorities on a couple of other things.
B.
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