[mira_talk] Re: 500Mb assembly

On Donnerstag 10 Dezember 2009 Filip Van Nieuwerburgh wrote:
> 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

Hi Filip,

take another assembler. Though I never tried it, I'd put my money on the 
Celera assembler. 100 bp might be just long enough for it to get working 
halfway right.

This is out of MIRA's league, I wouldn't want to use more than 10 to 20 
million reads at the moment. You might also think of hiring half a dozen 
bioinformaticians for one or two years to get that thing assembled / finished.

And if you are the only one "who has been tasked" (mind the 't' :-) to 
assemble that thing in a month: don't walk, run away! Sheeeesh. Doing things 
right takes time (and manpower).

Regards,
  Bastien

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