Does using Java provide more flexibility and libraries for manipulating whole genome sequencing, in other words, what principal language to choose for WGS data manipulation?
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6.8 years ago
vassialk ▴ 200

Does using Java provide more flexibility and libraries for manipulating whole genome sequencing data, in other words, what principal language to choose for WGS data manipulation? I know the basics of several computer languages, want to make an app calling BBMap, SAMTools/GATK and VCFtools and producing a clear mutation report in PDF and RTF. Is Java better over Python or Ruby for that or should I switch to pure native C++/assembly, not  losing time on high-level errors in packages? When I say better I mean built-in functionality and availability of open sources and libraries for fast robust coding.

wgs software • 1.8k views
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want to make an app calling BBMap, SAMTools/GATK and VCFtools

what does that mean? a system() call ?

and producing a clear mutation report in PDF and RTF

most of the time, you don't need programming skills for this.

open sources and libraries for fast robust coding.

Fast? you want C+samtools

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6.8 years ago

Java is a good language for developing bioinformatic tools. It's not a good language for developing pipelines that call tools; in that case, speed is not really important because 99.9% of the time is spent in the tools, rather than the pipeline that wraps them.

If you want to call functions within Java programs, writing in Java is the best approach. But if you just want to execute the programs in a standard way, using their command-line parameters, use a scripting language. Absolutely do not use C or assembly for writing a pipeline.

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thank you

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