On this topic... I heard about R analysis for recalling the encoded Solexa image files (are these the Bustard files?). Is such a sophisticated base calling analysis also available for SFF files for the Roche 454 data?
The 454 error model (tendency for poly-nucleotide repeats) seems suitable for capturing in a HMM... is there facility in R to build HMM based read mapping? I think it could be very interesting to try to develop this. Cheers, Dan. 2009/7/15 Sean Davis <[email protected]>: > On Wed, Jul 15, 2009 at 12:21 AM, Purnachander <[email protected]> wrote: > >> Dear R-users, >> >> I'm working on assembly of DNA fragments. I'd like to know which "R >> packages" contribute towards assembly of fragments being sequenced. >> > > Hi, Purna. > > I don't think there are any specifically for that purpose. You might want > to look here for a relatively complete list of other software that might > suit your needs: > > http://seqanswers.com/forums/showthread.php?t=43 > > Sean > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
