Rust for Bioinformatics

The home of the awesome Rust for Bioinformatics community. We are disrupting the status quo! And we love #Bioinformatics and #rustlang 🦀🧬💻❤

[Rust for Bioinformatics @rust4bio]

Long-read sequencing means whole-genome alignments at scale, and the old tooling wasn't built for hundreds of genomes at once. wgatools handles conversion, filtering, variant calling AND visualization, all in one ultrafast Rust toolkit. 🧬⚡
🔗 https://t.co/VOqgcGDtw6

[Rust for Bioinformatics @rust4bio]

BigWig and BigBed files have been served the same way for a decade: statically, slowly. Bigtools is a full Rust rewrite for reading AND writing them, built for the local, fast-querying world we actually live in now. 📊https://t.co/QJQmMVM2wN
#RustLang #bioinformatics

[Rust for Bioinformatics @rust4bio]

Mass spec proteomics usually means Java or C++. Sage flips that: 100+ citations, 500k+ invocations logged via telemetry, and it's pure Rust. Proof this ecosystem isn't just sequencing tools anymore. 🧪🦀
🔗 https://t.co/evHDLoUuss
#RustLang #proteomics #MassSpec

[Rust for Bioinformatics @rust4bio]

Ever wish bioinformatics tools "just installed" the way modern package managers do? Meet bv: a uv-style tool manager for our field. Reproducible, Docker-backed, digest-pinned lockfiles included. The boring infra work that saves everyone's Friday afternoon!
https://t.co/6gsWmtj8zY

[Rust for Bioinformatics @rust4bio]

SIMD + Rust + pattern matching = Sassy, a small, sharp tool from @curious_coding et al., for fast sequence search. Proof that you don't need a giant framework to move the needle, sometimes you just need really well-written low-level code. 🔍🦀
https://t.co/J3kXTH9KEk

[Rust for Bioinformatics @rust4bio]

Genome annotations keep getting bigger (hi, ENCODE). GFFx is a Rust toolkit built to query and extract features from ultra-large annotation files fast, because grep-ing a GFF file at 2am should not be anyone's life. 🧬📂
https://t.co/MQiEPtWncP
#RustLang #bioinformatics #genomics

[Rust for Bioinformatics @rust4bio]

FastQC has run your sequencing QC since forever with Java runtime and all. Enter RastQC: a full Rust rewrite with all 12 classic modules, 3 new long-read ones, and a built-in dashboard. Same trusted checks, none of the JVM startup tax. ⚡
🔗https://t.co/mgF69jcK53
#RustLang

[Rust for Bioinformatics @rust4bio]

Whole-genome variant calling... on your laptop... in under 100MB of RAM. Rosalind (Rust, obviously) went viral on HN this year for doing exactly that, with byte-for-byte reproducible outputs and zero cloud upload. Your genome, your machine. 💻🧬
🔗 https://t.co/I90RREMfZr

[Rust for Bioinformatics @rust4bio]

🧬 Big news: myloasm, a metagenome assembler written entirely in Rust, landed in Nature Biotechnology. It untangles closely related strains in noisy long-read data better than anything before it. Rust doing science.
🔗 https://t.co/lkTWSI0j1m

[Rust for Bioinformatics @rust4bio]

kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML, and more with kmertools.
https://t.co/9ybFm9YmZz
#rustlang #bioinformatics

[Zed @zeddotdev]

Linux when? Linux now. 🎉🐧

For the last 6 months, our team and our open source community have been working hard to bring Zed to Linux.

As of today, we've released our first, official, stable build of Zed on Linux!

https://t.co/WbptRrpkQw

[Rust for Bioinformatics @rust4bio]

@zeddotdev is now available for Linux users. My first thoughts on using it are great!
#rustlang #bioinformatics
https://t.co/AQHxgyILfA

[𝕐 @nomad421]

Ok #rustlang folks; question! When you publish a crate, cargo visits each dual dependency (deps where you provide both a version and a GitHub url), and “cleans” them to just include the dependency on the https://t.co/mxJhWymvNk crate. Is there a way to get this without building?

[Rust for Bioinformatics @rust4bio]

@CamilleMrcht Great, Thanks!

[Rust for Bioinformatics @rust4bio]

@CamilleMrcht Thank you for the amazing work and great thread! Is there any link to the slides of this talk ?

[Rust for Bioinformatics @rust4bio]

diced: a Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes by @althonos.
#bioinformatics #Rust
https://t.co/JTWiMd7Imt

[Igor Martayan 🦋 @IgorMartayan]

For my fellow rustaceans in bioinformatics, I made a new crate to iterate over minimizers in a sequence. It supports custom hashers and bit encoding, and integrates the mod-minimizers introduced by @giulio_pibiri and @curious_coding!
https://t.co/N9VVjbmzcP

[Javier Santoyo @jsantoyo]

Bigtools: a high-performance BigWig and BigBed library in rust. #BigWig #BigBed #SequenceData #Rust #Bioinformatics
https://t.co/5pvlgAQKqx

[𝕐 @nomad421]

If you've joined our #rustseq GitHub organization, please check out the issues on the "planning-and-discussions" repo for a link to join our Zulip channel! If you're interested in joining the #rustseq organization but aren't a part of it yet, please reach out!

[Rust for Bioinformatics @rust4bio]

Do not miss fairy, the new tool by @jim_elevator and @YunWilliamYu.
Significant speed improvements in sight for metagenomic binning!
https://t.co/qSnBj4Dtsf
#rustlang #bioinformatics

[Jim Shaw @jim_elevator]

We (me and @YunWilliamYu) built a fast coverage calculator for *multi-sample metagenomic binning* called fairy.

Available on github (https://t.co/JN4a0bHwVH) and as a short paper on bioRxiv:

https://t.co/PrGLy8LOlT

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