Thank you for rapid reply. With comparison to newbler and celera, mira is the absolute winner ( for data i have). It is completely off the topic, but what if i have some EST sequences that i do not know which technology has been used for sequencing(Sanger-454..), i did some test with mira --job=est,.. for Sanger and 454 independently. There seems to be no difference b/w results. Any suggestions? From: bach@xxxxxxxxxxxx To: mira_talk@xxxxxxxxxxxxx Subject: [mira_talk] Re: Where is my assembly at? 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