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Software update

Some updates :

Picard-Tools 1.79

Still an impressive update rythm (4 in less than 2 months), every time changes remains minor. (No worry)

GATK 2.2

This tool is reaching stability. In fact I used it to call variant on my project (Both unified genotyper and HaplotypeCaller). Despite some periods where updates came twice a day (a bit worry-some in fact), I had no real problems, fixes were mostly dealing with particular features or kind of data. So I guess we can consider this new version as mature enough.
Computations time is still a concern (You should not expect to get results on a big project within hours ;-), I hope that at some point multi-threading could work for all the tools (This would allow a better use of clusters).

ifort 13

To me the best fortran compiler, came up with few improvements, new Fortran 2003 et 2008 features, an enhanced MKL, and a better support for recent processors.

Cuda 5.0

The release promise efficiency improvements and a bunch of new features to ease development using CUDA. As a Fortran programmer, i am really eager to see alternatives to PGI compilers to easily take advantage of CUDA.


This project announced (and discussed) some time ago here and here and has been officially released at the end of august. This effort to come with both a new “method”  and accompanying tools should really be acknowledged. I tried stan while it was still in beta release and had no problem running  the examples. Despite compilation doesn’t frightened me at all, I believe the Rstan package is a good initiative as it may attract a wider audience. Some people had already played a bit here and there, with some classical example. I wish I could find time to do the same with an example in our field !

Categories: emacs, Linux, NGS
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