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