[mira_talk] Re: Regarding Time-estimate of mira

  • From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 6 Jan 2011 22:03:07 +0100

... or maybe it is low coverage and/or metagenomic ... these kind of
assemblies may take ages (I had a metagenomic dataset with some 2.4mio reads
.. it took 3 weeks to finish without parameter tweaking on a machine with
lots of RAM).

cheers,
Sven

2011/1/6 Bastien Chevreux <bach@xxxxxxxxxxxx>

> On Donnerstag 06 Januar 2011 Ganga Jeena wrote:
> > Happy New Year Michael,
> > For a genomic 454 data in accurate mode, My program din't proceed with
> the
> > contig formation since twwo days for  million reads.
> > How should I go about it?
> > wd splitting the data further to lesser number of reads for assembly in
> >  mira and then contigs into cap3 for further assembly a better idea ?
>
> No. Read
>
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_hard
>
> and find out whether repeats are causing trouble. The fact it is a simple
> genome assembly with 1 or 2 million reads
> and it takes so long is a bit troubling.
>
> Also, you switched off loading of XML info, that is even more troubling. My
> first gues is that adaptors/linkers are
> severely contaminating your project. Also search for those.
>
> B.
>
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