[mira_talk] Re: data over-load

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 23 Feb 2009 01:36:52 +0100

On Wednesday 18 February 2009 Giuseppe D'Auria wrote:
> I am working with a big big 454-titanium assembly and I had an overload
> of data resulting in a coverage around 150X (quite exaggerate).
> some body knows if there is some tool that, similarly to convert_project
> of caftools (that allows reducing the alignment for minimum coverage and
> minimum length of contigs), can reduce the contigs for redundant reads
> for example cutting the contigs at a specified value of coverage?

Hello Guiseppe,

well, this scenario can happen only with the new sequencing technologies ... 
normally people complain only about not enough coverage :-) However, why do 
you want to reduce the coverage anyway?

I've tried to think of a known tool that does what you want or to think of a 
simple way to realise what you're looking for, but found nothing really 
obvious or easy to implement.

The only "simple" solution that occured me is to filter already at the input, 
taking only every third or fourth read of your data. But this is not 
equivalent, you might loose parts that have a lower coverage and I'd refrain 
from doing that if possible.

Regards,
  Bastien

PS: "convert_project" is part of the MIRA package, not of the caftools from 
Sanger Center :-)

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