[mira_talk] Re: Metagenome assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 26 Apr 2012 22:53:45 +0200
On Apr 25, 2012, at 22:44 , Shaun Tyler wrote:
> Does anyone have experience assembling metagenome data with Mira. I have a
> feeling this might be one of those applications that will give Mira a nervous
> breakdown. The data is 100 bp paired end Illumina reads from libraries
> derived from nasal swabs. There is slightly in excess of 2 Gbp of data per
> sample (25 M reads or so).
>
25m reads alone are not a big problem, I've done RNASeq assemblies with 40 to
50m and I know at least two users who ventured into the 100m area (but I'd not
recommend doing that). You just need a machine which is big enough.
However, I fear that some aspects of metagenomes will indeed lead to problems.
If you assemble the date in "genome" mode, I think MIRA will have a hard time
in guessing the "coverage" of this "genome" ... and that will lead to
misassemblies. If you assemble in EST mode, things will probably go faster, but
there again I am almost sure misassemblies will happen.
The thing is: in metagenomes, there is no such thing as an "average coverage"
because this "average coverage" will be mainly driven by population ratios. I
have no idea how to get around this.
In any case: if you are making trials, set
-SK:bph=31
This will probably greatly reduce misassemblies at the expense of genomes with
low abundance being less well assembled.
Would love to hear back from you on that.
B.
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