[mira_talk] Re: Solexa Assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Jan 2011 19:37:19 +0100
On Monday 17 January 2011 17:13:55 Lionel Guy wrote:
> Think that 2x100bp solexa reads with 200bp insert size are in total 400bp,
> shorter than the median size of 454 Titanium reads. Any repeat longer than
> that won't be further solved.
>
> If you want to assemble further, sequence a mate-pair library with longer
> insert size, preferably several (e.g. 3, 8, 12, 20 kb). I can't see any
> way of closing further gaps by bioinformatics means only.
Yep, that was my main line of thinking when writing that extending 454 contigs
with Solexa data would be "improbable."
There is one case where that is possible though: sometimes, 454 sequencing has
problems at very specific, not necessarily repetitive sites in DNA and produces
only little, if any, reads there. Then another sequencing technology (Solexa,
Sanger, whatever) may help as it is not often the case that two sequencing
technologies have the same problems in coverage.
B.
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