Forum:Rust bioinformatics projects ideas

Question

[bompipi95]

Hi everyone,

I wish to work on a bioinformatics project to pick up Rust and to improve my computer science / programming knowledge in general. I don't mind reinventing the wheel a little bit, since my main goal is to learn the language and demonstrate knowledge via a project. I have experience in R, python and work primarily in RNA/scRNAseq data analysis, being a biologist turned bioinformatician. Could you suggest a useful & accessible project to start with? I am thinking of projects like speeding up an existing tool / developing more efficient bam parsers etc.

Thank you!

[barslmn]

Check out the projects on GitHub:

https://github.com/search?q=bioinformatics+language%3ARust&type=Repositories

https://github.com/search?q=bam+language%3ARust&type=Repositories

[bompipi95]

Thanks for the reply! Do you suggest working on existing rust tool repositories (e.g. submitting pull requests), rather than developing a tool separately?

Answer 1

[ATpoint]

I would start reimplementing something with a comparably limited codebase such as seqtk. It's a great parser with several submodules yet not overly complex compared to something like an aligner or the VEP. It's heavily used and fast so you can benchmark against its C implementation.

[bompipi95]

Ah yes, great suggestion!

Answer 2

[Jeremy Leipzig]

https://github.com/Ensembl/ensembl-vep

One of the most common tools used in all of bioinformatics, written in Perl.

[ATpoint]

Could you suggest a useful & ====>accessible<==== project to start with...

[Jeremy Leipzig]

parts of this could be ported over piecemeal

[bompipi95]

Thanks Jeremy Leipzig for the suggestion! Perl is unfortunately above my head at the moment, and working on this project would require me learning 2 (!) languages.. I will probably choose something else to work on! Maybe porting over something written in python/R is best for me to start with.

Answer 3

[cmdcolin]

it's hard to recommend what to write but here are two small CLI projects i made with rust https://github.com/cmdcolin/vcfverifier https://github.com/cmdcolin/secondary_rewriter use htslib or noodles for BAM/CRAM parsing (or parse the output of e.g. samtools view in SAM format as text. secondary_rewriter just parses the text, and vcfverifier actually uses htslib for bgzf file parsing).

i don't know a lot about single cell sequencing but since you do, try to add your expertise! calculate expression or coverage per-cell from a BAM file or something like that perhaps

[bompipi95]

Thanks for the thoughtful reply and suggestions! It's very useful & kind of you to share your personal rust projects. This is something I aspire to do!

Answer 4

[Jeremy Leipzig]

https://github.com/algolab/pantas

This probably should not have been written in Python (it takes 2 hours to run), but the fact it was gives someone an opportunity to port this over