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Yeah, there is actually a pretty big shift towards Rust in the comp bio / bioinformatics community. Nature even wrote a feature article about it a couple years
by samuell 5mo ago
Yeah, there is actually a pretty big shift towards Rust in the comp bio / bioinformatics community.
Nature even wrote a feature article about it a couple years ago:
Why scientists are turning to Rust
https://www.nature.com/articles/d41586-020-03382-2 https://www.nature.com/articles/d41586-020-03382-2
They mention the Rust-Bio [1] project by well known Snakemake author Johannes Köster & co, and there are some other widely used libraries like needletail [2] and noodles [3].
A cool smaller tool developed by performance wiz Ragnar Groot Koerkamp which was just published is Sassy [4] [5]. He has also been involved in developing some high performance SIMD based stuff (minimizers) [6].
[1] https://github.com/rust-bio/rust-bio https://github.com/rust-bio/rust-bio
[2] https://github.com/onecodex/needletail https://github.com/onecodex/needletail
[3] https://github.com/zaeleus/noodles https://github.com/zaeleus/noodles
[4] https://github.com/RagnarGrootKoerkamp/sassy https://github.com/RagnarGrootKoerkamp/sassy
[5] https://academic.oup.com/bioinformatics/article/42/5/btag244/8691840 https://academic.oup.com/bioinformatics/article/42/5/btag244...
[6] https://github.com/rust-seq/simd-minimizers https://github.com/rust-seq/simd-minimizers