On Monday 06 April 2009 Lionel Guy wrote: > [...] > It was much better using the parameters in the right order (placing my Yep, the order is important. "--job=" sets a whole bunch of stuff trying to do "the right thing". > My project: > - sequencing a complete bacterial genome (~2Mb) > - half a 454 Titanium run (~100Mb of data, not quite as much as > advertised), plus 2 lanes from a titration run. > - about 50k paired-end mates (experimental 20kb library) > > The bacteria that I'm sequencing experiences some kind of weird > alternate replication in late growth-phase, leading to an (at least) 2 > fold amplification of about 10-20% of the genome, which may impair the > uniform read distribution (I tried with urd:yes, and yielded strange > results). Alternate replication in late growth phase? Sheeesh ... that's some weird but interesting concept for a bug. I have a new assembly engine in alpha test right now. It still has problems with sequencing bias in unpaired data, but it rocks when paired-end reads are available. The 50k PE reads might be a bit on the low end, but I'd be interested to know how it fares with that kind of data you have. Please drop me a line if you're interested to run a test with the new stuff in development. Regards, Bastien -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html