[mira_talk] small contigs in first pass
- From: "Reith, Michael" <Michael.Reith@xxxxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 12 Jan 2010 20:09:00 -0500
Hi Bastien and everyone,
I'm doing an assembly of a lower eukaryote (genome ~35 Mb) using 454 sequences
and 76 bp Illumina reads (~1.2M & 20M sequences, respectively). Mira is just
in the first pass through the data, but has been writing the contigs of the
*_out_pass1.caf for more than a day now. The first 3500 or so contigs look to
be useful (>500 bp, something approaching the expected coverage), but since
that point the vast majority of the contigs are short with low coverage and
recently, they're mostly 2 Illumina reads. I'm now past contig 60000 and there
still appears to be a long way to go (>1.4M unused reads...= 700,000 2 read
contigs?). I'm wondering if there's a command line switch I can use to avoid
the generation of these small, probably useless contigs during the mira run (I
know they can be filtered out afterward). Or should I just use a half or a
quarter of the Illumina reads in doing the assembly? Any help or advice would
be appreciated.
Thanks,
Mike
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