Forum:In 2022 is Perl and Ruby programming languages still useful for bioinformatics?

Question

[narendra75]

What are the top 5 programming languages needed for bioinformatics 2022, apart from Perl and Ruby?

[Joe]

I probably wouldnt say ruby is in the top 5 for bioinformatics anyway.

[WouterDeCoster]

and with '2022', neither is Perl, except some legacy code

[Juke34]

Not focusing on bioinformatics but very interesting: https://qvault.io/misc/popular-coding-languages-2021/

[kojix2]

One of the greatest pleasures of using a minor programming language is that there is nothing to prevent you from reinventing the wheel. For example, if you were using Python, you would immediately be told that you don't need to create that tool because it already exists. But actually, reinventing the wheel is a lot more fun than you might think. Even if it is full of bugs. (Of course, using it in a real project may not be as much fun.) Translated with www.DeepL.com/Translator (free version)

Answer 1

[ATpoint]

This one here contains an (almost) complete list of all threads discussing this on Biostars:

Best programming language for bioinformatics - R Language

The last one on the list is the I think most recent one with excellent answers, written in 2020, not much change compared to 2022 I think. This one here:

Rust or C++, what to learn after Go for high-performance bioinformatics tools?

[shenwei356]

After 14 months, I still haven't started learning rust, but learned Go assembly to improve the performance of some core functions of a project :(

Answer 2

[colindaven]

I see these languages most - just my opinion, and not in any order, so just put yours instead of disagreeing :-)

High performance

• C / C++
• Java
• Rust
• Fortran (in R packages)

Most usable - data analysis

• R
• Python

Legacy

• PERL

Answer 3

[Juke34]

I will go with my own view:

Level3: Mainly computational biologist (high performance)

C / C++ / Go / Rust / Julia

Level2: Mainly bioinformatician (data analysis, scripting, tool with no need of high performance)

Python / PERL / Ruby / R / JavaScript / Java

Level1: Mandatory

bash / zsh

[ATpoint]

Out of interest, can you name three tools implemented in Haskell?

[Juke34]

^^ right, it was based on discussion with computational biologists. They see good potential with Haskell, Lisp, Scala... but still not so much used in 2022.