[mira_talk] Re: Reference vs. De novo assembly.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 10 Dec 2009 19:23:45 +0100
On Dienstag 08 Dezember 2009 Andrzej N wrote:
> As you can see now I have biggest contig 50000bp, but the "problem"
> remains. Is there any chance to tell MIRA not to add more sequences above
> the for example 100x? Here as you see in some single regions MIRA is
> putting 899 (I think is a limit of MIRA to put stuff on top of each
> other). Can we tell MIRA stop doing it?
You can't at the moment. MIRA keeps repetitive sequences in 'normal' contigs
at normal coverage, but for contigs only made of 100% identical repeats it
stacks everything together (if there was no way to disentangle using paired-
end).
I also had MIRA disentangle these 'repeatcontigs' at one time, i.e. if 12 rRNA
stretches were present in a bacterium it made between 10 and 13 rRNA contigs,
but then MIRA lost in those wannabe assembly benchmarks which only look at N50
and number of contigs. So I removed it.
I still feel that disentangling them is the right way to go though.
> This somehow artificially increases my coverage...
> I don't know if it that important, but doesn't look good.
It does not really increase your average coverage, perhaps by 0.1 or so. Not
really important.
> Do you have other suggestions, before I will go and start doing cloning ;).
Not really.
Regards,
Bastien
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