[mira_talk] High GC genomes and mira
- From: Phillip San Miguel <pmiguel@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 17 May 2011 11:15:59 -0400
On 5/16/2011 1:17 PM, Bastien Chevreux wrote:
On May 16, 2011, at 15:16 , Phillip San Miguel wrote:
I tried MIRA V3.2.1.15 on a 70% GC bacterial genome (Deinococcus) at
around 100x coverage with solexa PE 101 base reads. My N50 contig
size was 4630 bases. That seems short to me, but it might be a result
of the 70% GC. So I decided to de novo assemble a 50% GC data set
from the same run.
That's bad, really bad. You are the second report I get that
apparently, MIRA has problems with high GC Solexa data sets. The first
being a supersecret bug of a big company, I cannot get the data to see
what's causing havoc. Would it be possible for me to have a look at
that thing? No promises, but it might help.
B.
Probably, just let me check with the owner of the sequences.
However, the short contig lengths may derive from something
trivial: read distribution bias. An Eland/Gerald mapping of our Illumina
Salmonella reads produces a reasonably even coverage depth across the
the genome. A similar mapping of our Illumina Deinococcus reads shows
mostly 50-150x coverage, but also frequent regions with very low
coverage (a few X coverage -- or zero).
--
Phillip
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