[mira_talk] Re: Where is my assembly at?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 25 Sep 2011 15:34:33 +0200
On Sunday 25 September 2011 15:23:23 Visam Gültekin wrote:
> It might be inappropriate question, but why do you think MIRA is not
> suitable for plant genomes?
>
> I have a 454 data for two plants ( 454 titanium, not paired end) and MIRA
> is doing good, I am awaiting reply with great curiosity
Oh ... my bad. Wrong wording. In fact, I also to plant RNASeq de-novo assembly
now (oh the fun).
Let me rephrase my statement.
I think that MIRA is suited for de-novo assemblies with
- Sanger reads: 5 to 10 million
- 454 reads: 5 to 20 million
- Ion Torrent reads: 5 to 20 million
- Solexa reads: 15 to 30 million (perhaps 50), provided the coverage is <= 80x
to 100x
PacBio is not yet in the list above, I need more data to give good estimates.
The above is usually OK for prokaryots and most lower eukaryots, however most
plants and higher eukaryotes need larger data sets for de-novo.
Artemus had 165 million Solexas for his assembly ... and there I have the
distinct feeling that MIRA will choke at one point or another.
Best,
Bastien
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