Forum:Programming languages in industry

Question

[m.monikus]

Hello,

I am aware that this forum has a lot of threads on which programming languages are relevant for bioinformatics. However, I would like to ask those of you who work in industry what currently the trending languages are that make sense to learn. I assume most bioinformatics people who are remotely working on NGS and similar topics know R and bash to some extend. In industry, for a data analyst role, what else would you recommend and why? Please be so kind and indicate whether you are working in industry yourself. Cheers!

[Jean-Karim Heriche]

As far as I am aware, bioinformaticians make use of the same tool set regardless of where they work. Some places may impose some constraints on your choice of languages or tools but unless they want you to rewrite entire libraries, you'll be working with the same ones as everybody else.

Answer 1

[Medhat]

• Python (Data analysis and Machine/Deep learning)
• Pipeline building Snakemake or Nextflow (most industry lean to work with Nextflow)
• Compiled langue C/C++, Go, Rust (I see Rust appears more now beside C/C++)
• Something I did not write earlier because I assumed it is fundamental, Data structure, and Algorithms, they are a must to write efficient code and solve problems

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Update I did not mention R in my answer, because the question mentioned it.

[Jean-Karim Heriche]

I would add R to this list (see e.g. here and here)

[Medhat]

Indeed, but the author already mentioned it, so I avoid duplication, I think maybe I should to update my answer to make it clear. Thx!

Answer 2

[Mensur Dlakic]

To cover 100% of industry needs, you'd need to learn all the languages Medhat mentioned above, and probably a couple more. I don't think any candidate needs to have a skillset that covers 100% of industry need, so you should be fine by adding python to the ones you already mentioned. I don't work in industry so my opinion is not based on firsthand experience, but I think that a combo of Linux/bash, python and R should be more than adequate for >50% of all job ads out there, industry or not.

[Medhat]

The thing I did not mention, and I see it becomes the main thing; working with cloud computing (whatever it would be Google, AWS, ...).