Open source libraries for NGS data analysis.

Question

[mieszko91]

Hi! I'm trying to write a C# program to next-generation data analysis. Could you advise me how to get started, and which programming libraries i can use in my project? I know that .NEt is not popular platform for bioinformatic solutions, but i must write in this language. I want start by writing a code for reads quality control, short reads alignment and SNP locating. I'm only a programmer and I have no experience in this field. Could you advise me some well-documented libraries in C# or maybe C++ libraries (maybe i can try write a wrapper for them)?

Sorry for my english.

[lh3]

For algorithm-centric components, seqan is helpful. For format parsing, htslib is useful. Don't waste your time on a typical short read aligner unless you just take that as an exercise. Also don't understand why you "must write in this [C#/.NET] language".

[mieszko91]

Why i shouldnt waste time for short read aligner?

Answer 1

[Sukhi Singh]

I came across Seqan once, could be useful for you (open source, C++) -> their GitHub and paper.

Another useful post C++ libraries for NGS data and such

[mieszko91]

Have you heard about the library in C # that I can use? I must integrate NGS solutions with .NET enviroment