[mira_talk] Re: MIRA: I am doing it wrong.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 7 Dec 2009 19:37:17 +0100
On Montag 07 Dezember 2009 Edith Schlagenhauf wrote:
> as I am working on a 67% GC content genome assembled from 454 Titanium
> reads generated in the specified time range, I am wondering what you
> exactly meant by this statement?
Well, if a simple bacterium (66.5% GC) was sequenced at ~45x coverage and
still generates something like 900 (!) contigs with something like 3 megabases
consensus, then you know something's wrong.
A later sequencing with the same coverage but new ("improved" as Roche called
it) kit gave something like 80 contigs and 4 megabases of consensus.
Let's just say that there were some unforeseen consequences due to increased
read length in the Titaniums coupled with interesting secondary folding
effects of high GC sequences.
Regards,
Bastien
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