Hello All, I just finished my first assembly, it consists of only 454 FLX data, paired and unpaired. I used the manual at http://www.chevreux.org/uploads/media/mirav2939_454dev.html. I now have the following problem, the assembly stopped because of "megahubs". The relevant part of the output says : Total megahubs: 28773 MIRA has detected megahubs in your data.This may not be a problem, but most probably is, especially for eukaryotes. You have more than 0.0% of your reads found to be megahubs. You should sheck the following: 1) for Sanger sequences: are all the sequencing vectors masked / clipped? 2) for 454 sequences: are all the adaptors masked / clipped? To learn more on the types of repeats you have ... (to be extended) *ONLY* when you are sure that no (or only a very negligible number) of sequencing vector / adaptor sequence is remaining, try this: 3) for organisms with complex repeats (eukaryots & some bacteria): - use -SK:mnr=yes - reduce the -SK:rt parameter by 2 and try again (iteratively, down to 4) *ONLY* if the above fails, try increasing the -SK:mmhr parameter You have 0.5% of your reads as megahubs. You have set a maximum allowed ratio of: 0.0 Ending the assembly because the maximum ratio has been reached/surpassed. What should I do to get the assembly to finish ? 0.5 % of bad reads doesn't sound that bad, does it ? -- Dag, Jan