[mira_talk] Re: 454 and solexa pared-end

On Thursday 09 April 2009 Jan Paces wrote:
> I cannot find guide how to run mira on 454 shotgun data and solexa paired
> end. Please, can someone help? I think I read something about it - how to
> prepare solexa paired-end data. But I cannot find it anymore.

Hello Jan,

sorry for the long delay and the shortness of this reply. I've been on a short 
vacation and have now a pretty tight professional work schedule until the 
week-end.

There no such guide :-) I refused until now to think of de-novo assembly with 
36mers. Now that SOlexa has 76mers (and with a pretty good quality), I have 
started work on de-novo hybrid 454/Solexa assembly.

Current best alternative so far: assemble the 454 sequences and use these as 
backbone for a Solexa mapping. Or use Velvet or any other Solexa de-novo 
program, fragment that data and mix with the 454 reads. Then use that for a 
mapping with the Solexa data.

All of these approaches already work quite well. Not ideal, but doable.

Regards,
  Bastien


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