Hi Bastien, hehe, you had busy night to answer all our emails. Thanks 8) Bastien Chevreux wrote: > There no such guide :-) I refused until now to think of de-novo assembly with > 36mers. Now that SOlexa has 76mers (and with a pretty good quality), I have > started work on de-novo hybrid 454/Solexa assembly. > I am really looking forward to. We are using 36mers for mate-pairs paired-end on solexa, because 76 mers seems to have too much chimeras in them. For 36mers there is ~1% chimeras, for 76mers >10%. From the technology point of view (preparation of the library) I think you cannot get rid of them. 76mers are ok for normal paired-end, but then your insert size is ~500, which would be almost covered by one 454 read and IMHO this kind of paired-end do not really improve assembly. For longer insert sizes on solexa people are now stuck with 36mers - until solexa starts to use linker to find exact position of ligation (like 454) or some other trick. > Current best alternative so far: assemble the 454 sequences and use these as > backbone for a Solexa mapping. Or use Velvet or any other Solexa de-novo > program, fragment that data and mix with the 454 reads. Then use that for a > mapping with the Solexa data. > > All of these approaches already work quite well. Not ideal, but doable. > I tried this, but it looks mira do not use paired-end info from solexa reads to join appropriate contigs or to split wrong assemblies (which is probably not possible in mapping). Am I right or I set it up wrong? Also when using output from velvet, I loose that valuable paired-end information. Well, mira is best, I'll wait for new version. I have real-life data and I will do beta-testing, if needed. Thanks, Jan -- 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