Trying several tools is always a good thing. However, merging assemblies is a notoriously difficult problem.
On 12/05/2012 01:54 PM, Forster, Robert wrote: > Sebastien: > > The LibraryStats indicates AverageOuterDistance of 185, SD 38, number of > sequences 72753702 > > I'm running now with different kmers. Our original run with Ray 2.0.0-rc8 on > (I think) 30 cores took 3 days 5h on a Dell server. I upgraded the Ram on my > little cluster (using 49 cores) so it will run Ray and it's now taking 11-13 > hrs with Ray-2.1.0 :). Big change! > > There is quite a difference in largest contig. I'm wondering whether it is > legitimate to merge assemblies like some other groups do when assembling with > velvet or Soap? > > > Ray 2.1.0 > Original kmer 21 Ray rc.2.0.8 Cray kmer 21 > kmer 31 kmer 45 > Contigs >= 100 nt > Number 3500538 2817095 5974696 > 7161038 > Total length 624475006 > 510215305 945838381 1026747597 > Average 178 181 > 158 143 > N50 168 > 166 146 129 > Median 125 122 > 116 110 > Largest 44799 66893 > 102879 80250 > Contigs >= 500 nt > Number 113898 101609 > 110394 74935 > Total length 120187394 > 116199542 117723390 75591030 > Average 1055 1143 > 1066 1008 > N50 1102 > 1247 1109 1006 > Median 738 776 > 723 692 > Largest 44799 66893 > 102879 80250 > Scaffolds >= 100 nt > Number 3496328 2813404 > 5970969 7158055 > Total length 624949147 > 510625699 946272789 1027132935 > Average 178 181 > 158 143 > N50 169 > 166 146 129 > Median 125 122 > 116 110 > Largest 49246 86011 > 102879 98547 > Scaffolds >= 500 nt > Number 111320 99299 > 108265 73363 > Total length 121336504 > 117181056 118823565 76572975 > Average 1089 1180 > 1097 1043 > N50 1160 > 1313 1164 1065 > Median 743 782 > 727 696 > Largest 49246 86011 > 102879 98547 > > -----Original Message----- > From: Sébastien Boisvert [mailto:sebastien.boisver...@ulaval.ca] > Sent: December-05-12 11:16 AM > To: Forster, Robert > Cc: denovoassembler-users@lists.sourceforge.net; Jacques Corbeil > Subject: Re: Ray meta? > > What do you see in LibraryStatistics.txt ? > > This file contains auto-calibrated insert size by Ray. > > ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
