[Bio-Linux] Bio-Linux updated image and new packages

[Tim Booth]

Hi Andy,

> Thanks for the reply. 
> I can see the issue with setting the Kmer setting upto 96. I hadn't
> realised that if compiled at 96 but only used a Kmer of 64 it meant an
> increase in memory usage compared to compiling to at 64 Kmer.

It's hard to see how big a difference this will make in practise.  I'd
need to run some test data on both versions and see how it actually
impacts the memory usage.

> I have downloaded and compiled from source at a higher Kmer and it is
> a relatively painless task and matter of following their online
> instructions.

Yes, the thing compiles quite happily, so the Bio-Linux package doesn't
add much aside from a bit of convenience.

> I personally think that the having a default maximum Kmer of 96 would
> be better as with the increase in reads of upto 250 bp then having the
> ability to use a kmer of upto 96 "out of the box" will give "better"
> assembly. My experience from doing bacterial assemblies is that
> programs such as Kmergenie often predict the optimal Kmer is above 64,
> so would be advantageous to have the ability to use higher Kmer.

OK, I'm convinced.  Some people are always going to need to need to
recompile, as some people will want a lower-memory version or super-long
Kmers, but it's more important that the default version can deal with
typical data.  I'll modify the default in the package.

Cheers,

TIM

> Dr Andrew Millard
> Division of Microbiology and Infection
> Warwick Medical School
> The University of Warwick
> Coventry
> CV4 7AL
> http://www2.warwick.ac.uk/fac/sci/lifesci/people/amillard
> Tel 0247615045
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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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OX10 8BB 

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