Hi Isabelle, Out of so many precious and experienced members of this talk-list, i should not be advising, but i ran into same problem before. how did you get rid of contamination? i am asking this because, it took me some time to figure out the solution, that was giving me hard time with my data.. just after that, i mean when one is fully confident of preprocess, you can set allowed megahub ratio with -AS:mmhr= integer . you can see the ratio you are facing in the very same complain of mira.. Best,Visam.. Date: Tue, 20 Mar 2012 14:36:58 +0100 Subject: [mira_talk] megahubs in MIRA From: isabelle.lesur.kupin@xxxxxxxxx To: mira_talk@xxxxxxxxxxxxx Hello, I am trying to perform an assembly consisting of 84 086 Sanger reads with qualities. I used the following command: -bash-3.2$ mira --project=OCV2_prime_full_length --job=denovo,genome,normal,sanger --noclipping=all --notraceinfo SANGER_SETTINGS And the assembly stopped bacause of Megahubs. Total megahubs: 8 I followed the recommandations MIRA gave me: - I checked for vector/adaptor sequences - I set the -SK:nrr parameter as follow: -SK:nrr=10 and -SK:nrr=20 and -SK:nrr=30 The number of megahubs reached 66 with the -SK:nrr parameter - I used the -SK:mmhr parameter This time, the number of megahubs reached 74 I then used RepeatMasker to mask the repeats in my sequenced and clipped all the Ns. This time, I ended up with 66 megahubs.... So, does anybody know how I could get read off these megahubs??? Thank you for your help! Isabelle