[mira_talk] Re: 500Mb assembly
- From: "Filip Van Nieuwerburgh" <Filip.VanNieuwerburgh@xxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 10 Dec 2009 18:48:57 +0100
Hello Greg,
I checked the repeats in the most closely related genome (honey bee).
The biggest repeat was around 2000bp.
Kind regards,
Filip
From: mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Gregory Harhay
Sent: donderdag 10 december 2009 18:44
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: 500Mb assembly
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 won't 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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