[mira_talk] Re: 454 and solexa pared-end
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 14 Apr 2009 23:28:32 +0200
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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