[mira_talk] Re: 500Mb assembly
- From: Gregory Harhay <gregory.harhay@xxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 10 Dec 2009 11:44:21 -0600
Fillip:
How big are the repetitive regions in the insect genome? I they are larger
than 3000 nt, your paired-end reads will only take you so far .. Your
contigs won¹t scaffold completely no matter what assembler & scaffolder you
are using as they will be chopped up by the unbridgeable repetitive regions,
unless of course, there is some other physical evidence joining the contigs.
Greg
On 12/10/09 9:39 AM, "Filip Van Nieuwerburgh"
<Filip.VanNieuwerburgh@xxxxxxxx> wrote:
> Dear,
>
> I have been asked to de novo assemble an insect genome.
> Until now, I only de novo assembled bacterial genomes (max 5 Mb). Mira proved
> to be the best assembler (in my hands) to tackle these assemblies.
>
> What would be the best strategy (also taking into account that I cannot wait
> more than a month for MIRA to finish) to de novo assemble the 500Mb insect
> genome?
> I have:
> - 100E6 reads of 2x100 bp Illumina data
>
> - 1 full Roche titanium run: paired-end insert size= 3000 bp.
>
> - A 16 core 64-bit linux with 128Gb of RAM
>
>
> Thank you!
>
>
> Kind regards,
> Filip
>
>
>
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