[mira_talk] Re: Denovo assembly of a high GC bacteria
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 18 Mar 2010 21:34:16 +0100
On Donnerstag 18 März 2010 Martin A. Hansen wrote:
> I have 2M 454 titanium reads (~500bp in length). GC content is 65% (!) and
> genome size is 7Mb.
>
> I have a fairly good assembly done with Newbler:
> [...]
> So I wanted to do an assembly with Mira to compare the assemblies. I
> followed the Mira 454 tutorial (sff_extract and remembering to include
> quality and traceinfo!) and simply ran with the following options:
> [...]
> But the result is disappointing:
> So, any suggestions?
I suppose the standard config does not cope very well with high coverages as
you have (~100x), it's is geared towards more 'normal' coverage. I suppose
that this together with the high GC will lead to many false positive repeats
detected.
Hmmm ... could you please try adding
454_SETTINGS -CO:mrpg=20
and tell whether this improves the assembly?
Regards,
Bastien
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