Hi,
Hmm interesting. This is indeed the reverse-complement. But you don't
output those normally right?
There are also some where they are exactly the same:
1 825006 1 825006 825006 825006 100.00 825006 825006
100.00 100.00 contig-859 contig-539
Best regards,
Ino
On Fri, May 16, 2014 at 3:44 PM, Boisvert, Sebastien <boisv...@anl.gov>wrote:
> > 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
> >
> >
> >
> >
> >
>
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