> From: Ino de Bruijn [ino.debru...@scilifelab.se] > Sent: Friday, May 16, 2014 7:31 AM > To: denovoassembler-users@lists.sourceforge.net > Subject: [Denovoassembler-users] Duplicate contigs? > > > > > Bonjour, > > I have assembled a simulated metagenome of 20 genomes. I have 64 pairs each > containing 23,5M pairs. I have been using Ray v2.3.1 using 2048 cores. > > For one of the genomes I seem to be getting duplicate contigs. > > > I have mapped the assembly against itself using MUMmer and found out that > some of the contigs are exactly the same. MUMmer shows these kind of hits: > > > [S1] [E2] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [COV R] [COV Q] > [REF] [QRY] > > > 1 825006 825006 1 825006 825006 100.00 825006 825006 > 100.00 100.00 contig-859 contig-717 > > > For an explanation of the format: > http://mummer.sourceforge.net/manual/#coords >
I have seen cases where there was a significant overlap between two contigs and for which Ray failed to merge them. I have not seen the case where there are 2 identical contigs (in your case, one is the reverse-complement of the other). > > Do you have any idea how this might happen? > > > Best regards, > Ino > > > > > ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
