[mira_talk] Re: Assembling 454 and Solexa mate-pair data - rethinking ...

On Montag 31 August 2009 Martin A. Hansen wrote:
> MIRA has been running for over a week now digesting this rather simple
> de-novo assembly:
> [...]

Hmmmm ... at which point is it? Should be through it, or almost.

Then again, it shouldn't take that long, even on machines from 2 years ago.

> Pseudo code mockup (with limited detail):
> [...]
> Memory consumption would be OK. Speed would be OK.
> How about it?

I'd do it a bit differently: throw out every read which aligns in a contig and 
is more than 3kb away from one of the ends. You might want to try a bit 
smaller hashes though, I'd try 30 or 25 first.

One drawback: it throws out repetitive reads where one repeat copy is present 
in the contigs.

Regards,
  Bastien


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