[mira_talk] Re: all my 16S in one contig
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 5 Mar 2012 13:03:04 -0500
On 2012-03-05, at 12:55 PM, Davide Sassera (davide.sassera) wrote:
> Dear Bastien and Mira ppl,
>
> I'm assemblying with solexa (100bp, paired) a 5,6 Mb genome, with 200x
> coverage.
>
> My problem is that all the copies of the ribosomal genes (16S, 23S, 5S) get
> assembled together in one single contig.
>
> Based on reference I think I should have 8 ribosomal operons, which agrees
> with the 8fold coverage of the "all the ribosomal sequences mashed together"
> contig.
>
> I have been thinking about possible solutions to this, but I then realized
> other people must have had the same issue, so why lose my mind when I can
> stand on the shoulder of giants?
Welcome… it's good to had enew blood.
In my opinion, I don't think that you can assemble a whole genome de novo with
just illumina reads, no matter what the coverage. There is not enough genetic
diversity in the stretch between the boundary of a repeat to the region of
unique coverage with illumina alone, even with standard paired reads - where I
believe the fragment sizes are 250-500 bp. I would recommend either mapping
this to a reference genome or getting 40-fold 454 coverage.
Speaking of coverage, I think 200x is over-kill, and would also lead to
misassembles - try 80x.
HTH,
John
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