Hi Bastien! I am not quite sure what teh combined mapping and de-novo assebly is; would this actually join the reference contigs? If so I should go back and read the manual better.. A mapping assembly could be ok for now, but in principle I am against this approach; In our genome projects we might have in the range of 10-100 shotguned PCR products (for eukaryotes I guess it might be much much more). Doing a mapping (as far as i understand) will break the assembly at all these sites, and they will then have to be manually joined, which is prone to human errors, and lacks all the nice features that the assembler has (detecting ambiguities, properly handle paired-end info etc.). The gloomy result might therefore be that you spend much time making your PCR:s assemblies and then fail to properly join your contigs in the end anyway. I think that a proper handling of really long sequences would be great in the gap-closure phase of a genome project. (This is also the only area where phrap is still beating MIRA...) B On Thu, 25 Jun 2009 19:43:23 +0200 Bastien Chevreux <bach@xxxxxxxxxxxx> wrote: > On Donnerstag 25 Juni 2009 Björn Nystedt wrote: > > [...] > > I think the megahub is actually an artefact; the single read in the megahub > > logfile is a long (15kb) fake read comprising a complete PCR product. (The > > complte run is 300000 GS20, 16000 Sanger and ~20 PCR fake reads) > > Ah ... the fake PCRs is some crucial info which was missing. Yes, that > explains a bit the behaviour. > > You sure you don't want to do a mapping assembly? Or a combined mapping and > de-novo assembly? > > 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 -- ==================================== Björn Nystedt (Sällström) PhD Student Molecular Evolution EBC, Uppsala University Norbyv. 18C, 752 36 Uppsala Sweden phone: +46 (0)18-471 45 88 email: Bjorn.Nystedt@xxxxxxxxx ==================================== -- 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