I agree with Jitendra, choosing programming platform is more personal and also depend on how long you are working with your favourite language. But for beginners, I would recommend python because of easier syntax and simple oops approach. Now python can be integrate with any language like Cython (with C),PyPy, PyR, etc and python now has very enrich library stores with which you can do anything. for NGS , python is highly recommended as many new good tools made recently in python. R is good for downstream analysis like doing statistical analysis, create fancy graphs(ggplot2), work with rnaseq data (Deseq,degseq,etc), pathway analysis, etc, however R itself just a statistical package not generally into programming lang. Ruby is also getting popular these days because of simple programming style. But someone want to master in programming should go for C/C++,java,C# or python.
I would recommend python and lower level language C because of easier syntax and simple oops approach. Moreover, I do a lot of boinformatics programming, but I don’t use any of the “Bio*” projects, as they never seem to have much that is of use to me, and what little is useful to me is easier for me to code myself than to install any Bio* project and deal with its idiosyncracies.
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