[mira_talk] Re: 454Ti, MiSeq250PE, HiSeq100PE Hybrid assembly..
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 6 May 2013 00:09:25 +0200
On May 5, 2013, at 23:59 , raw937@xxxxxxxxx wrote:
> I have a few metagenomes were I have data with all three platforms.
> I have filtered the reads for low quality, phiX, dimers etc.
Ummm … it is very rare that outside filtering produces a better assembly than
filtering with MIRA. Well, to be honest: phiX is something which will come only
in 3.9.16, but apart that: Illumina data should not be filtered or quality
clipped by other tools, MIRA does a much better job. For 454 data one should
take the clippings from the Roche software and then let MIRA do the rest.
> What are the command parameters for such an assembly? I have them still in
> fastq format.
You should take 3.9.15 (or better, wait for 3.9.16 out RSN). Then either
assemble in "genome" or "est" mode, depending whether your samples are real
metagenome or simply clean cultures of some different strains. You'll find
examples for setting up manifest files in the manual.
> I have 20million HiSeq100PE, 2million MiSeq250PE and a million 454Ti for
> about 8 samples. How much memory will I need?
Unknown, highly dependent on your data. As a rough approximation I'd say: not
below 48 GiB, but I may be wrong there.
> And, how many trends should I give mira? As I want to assemble it rather
> quickly.
Rather quickly is always subjective, 3.9.16 will again be a bit faster than
3.9.15 for that many reads.
Take something between 8 and 64 threads (if you have that many cores).
B.
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