Hello, Start with reading a MIRA manual: http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html Part about 454 sequences is important: http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_454 Usually you need to preproces data. After that you call mira with: mira -project=NAME_OF_PROJECT -job=accurate,denovo,genome,454 -- With best regards, Przemyslaw Gierski. From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Diogo Santos Sent: Montag, 25. Juli 2011 17:19 To: mira_talk@xxxxxxxxxxxxx Subject: [mira_talk] MIRA vs Newbler (454 est's) Hello I have received data from an EST's project from 454. they make the assembly with Newbler 2.5 and they get 5869 contigs (length>100) with coverage 11x (I know it's low, but it's what I get:( ). I try to use MIRA to make some testing and use the original data to reassemble, but I get a strange result (19378 contigs with length >100 and coverage 4x). Can you teel wich parameters should I change? Thanks Diogo Santos