[mira_talk] Re: Call for testing: MIRA 3.2.1.17 and Ion Torrent
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 16 May 2011 19:17:01 +0200
On May 16, 2011, at 15:16 , Phillip San Miguel wrote:
> I am now using MIRA V3.2.1.17 to de novo assemble 13 million solexa reads
> (101 base PE reads). That is 1.3 billion bases of sequence. The genome size
> is about 4.5 million bases (Salmonella). So that is 200x-300x coverage--more
> than I intended.
Do yourself a favour: go with 6m reads, that should be plenty enough.
> Anyone want to predict the N50 contig length?
Depends on the genome itself, how repetitive it is. With PE reads I would hope
for N50 >20kb though.
> 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.
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