[mira_talk] Re: miramem under-estimate
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 23 Nov 2010 10:04:15 +0000
On 23/11/10 07:45, Bastien Chevreux wrote:
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.
Hi, Bastien.
OK, I took your advice, and stopped my MIRA assembly of 20 x 10^6 50bp
paired-end Solexa reads from a bacterial metagenome - I'm now running:
mira -project=meta \
-fastq \
-job=denovo,genome,normal,solexa \
-GE:not=8 \
-SK:nrr=8
This is MIRA V3.2.1rc2 (production version).
MIRA has completed Pass: 1, with a memory footprint of 28.8GiB in ~12h.
Thanks for your help,
Tony.
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk/~ajt
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