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

[Millard, Andrew]

Hi Tim,

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.  
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. 
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.


andy  


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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