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Software update

Another quick review of updated softwares :

LLVM 3.2

The llvm suite gain a a lot of recognition and definitely deserve to be be tested. Freebsd10 will use llvm/clang as default compiler and  Nvidia nvcc compiler rely on llvm, which may make these tools in a near future an easy way to develop GPGPU applications.

Magma 1.3

A new release of magma, this version is now relying on cuda 5.0, more info are detailed here. A noteworthy point is that magma have started to work on Xeon Phi support.

Impute2  & shape-it 2

J. Marchini, talked about these releases at the 4th ICQG.  I’ll definitely give it a try.

Picard tools 1.83

After an impressive update rhythm (24 releases in 2012 !), 2013 seems to follow the same trend.

GATK 2.3

New run time improvements, more tools are now multi-threading enabled, more info available here. But…our bug regarding genotype calling is still not totally solved (let’s says a big improvement occured with version 2.3, but this is still not perfect).
For a deeper look at GATK 2 pipeline have a look at the presentation held at the GATK workshop.

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Categories: emacs, Linux, NGS
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