... or maybe it is low coverage and/or metagenomic ... these kind of assemblies may take ages (I had a metagenomic dataset with some 2.4mio reads .. it took 3 weeks to finish without parameter tweaking on a machine with lots of RAM). cheers, Sven 2011/1/6 Bastien Chevreux <bach@xxxxxxxxxxxx> > On Donnerstag 06 Januar 2011 Ganga Jeena wrote: > > Happy New Year Michael, > > For a genomic 454 data in accurate mode, My program din't proceed with > the > > contig formation since twwo days for million reads. > > How should I go about it? > > wd splitting the data further to lesser number of reads for assembly in > > mira and then contigs into cap3 for further assembly a better idea ? > > No. Read > > > http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_hard > > and find out whether repeats are causing trouble. The fact it is a simple > genome assembly with 1 or 2 million reads > and it takes so long is a bit troubling. > > Also, you switched off loading of XML info, that is even more troubling. My > first gues is that adaptors/linkers are > severely contaminating your project. Also search for those. > > B. > > -- > 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 >