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New to Bioinformatics - What language would you recommend?
I'm new to this bioinformatics thing, so I'd like to know what software or languages would you recommend to learn. Thanks 
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There is no single answer to this question, so I'll list some of the best-known languages in decreasing order of importance in bioinformatics.
#1 R, if only because of Bioconductor
#2 Python, most popular general purpose language. Could nearly replace R, if it wasn't for Bioconductor
#3 Java. Very wordy compared to Python, but if you want to build more complex applications, very useful.
#4 C++ For speed of performance, nothing can beat C++ (or C).
#5 BASH Useful to pick up a few tricks just to be able to work faster on Unix.
# Not even in the ranking. Perl. This language is condemned to disappear. Python is a superior language to Perl. The main purpose of learning Perl would be to decipher cryptic legacy code. -
Them is fighting words.Originally posted by blancha View Post
Actually the "best" language depends on what the original poster is going to do:
1) Just run bioinformatics packages -- Spades, Trinity, ABySS, Tophat, BBMap, etc? Then learn the supporting package such as Picard, BedTools as well as basic shell commands -- cut, paste, sed, etc. Mastering that list by itself will occupy a person for many years.
2) Manipulate and visualize statistics from the above packages or other people's work? R and bioconductor.
3) Present information to people via the web? Javascript or JQuery or similar.
4) Do text manipulation and comparisons? Python is as good as any.
5) Write new innovative programs dealing with complex problems? Java (or one of the variants), or C/C++. But really, most of the complex problems have been solved or are being solved by companies and/or larger institutions. If a person joins one of those active working groups the language will be dictated.
So "America CT" that is my opinion. Not knowing anything about you I suspect that #1 is what you want. Learn the tools already out there.Comment
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