Rust for Bioinformatics

kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML, and more with kmertools. github.com/anuradhawick/k… #rustlang #bioinformatics

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! zed.dev/linux

@zeddotdev is now available for Linux users. My first thoughts on using it are great! #rustlang #bioinformatics zed.dev/download

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 crates.io crate. Is there a way to get this without building?

@CamilleMrcht Great, Thanks!

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

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

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! crates.io/crates/minimiz…

Bigtools: a high-performance BigWig and BigBed library in rust. #BigWig #BigBed #SequenceData #Rust #Bioinformatics academic.oup.com/bioinformatics…

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!

Do not miss fairy, the new tool by @jim_elevator and @YunWilliamYu. Significant speed improvements in sight for metagenomic binning! github.com/bluenote-1577/… #rustlang #bioinformatics

I've released a new version of xgt (v0.3) which introduces the -k/--insecure option to disable peer SSL verification. This option should only be used when the GTDB's API has an SSL certificate. Enjoy! Share! #rustlang #bioinformatics github.com/Ebedthan/xgt

Please reach out if you are interested! Thanks @nomad421!

@shuttle_dev @Lisa_Crossman One of the early adopters in the sciences, or at least earliest experimenters. Also @rust4bio exists.

#RTD 21: Today is about `todo!` from the std lib doc.rust-lang.org/std/macro.todo…. todo! marks code paths you intend to implement, but haven't finished. In our example, it works with types to allow our code to compile (infers the proper type for the else branch)! play.rust-lang.org/?version=stabl…

2) recmap, which parses HapMap-formatted recombination maps, and interpolates the map at arbitrary positions. This is a library crate with optional command line tool. The CLI tool will interpolate recombination map positions and rates for a BED file github.com/vsbuffalo/recm…

Two bits of Rust software I've split off from another project so others can use them now: 1) genomap, which is a simple type for storing generic data indexed by a chromosome. Maintains smart chromosome ordering automatically (i.e. no more chr1, chr10). github.com/vsbuffalo/geno…

"We introduce Floria, a novel method designed for rapid and accurate recovery of strain haplotypes from short and long-read... based on minimum error correction read clustering , and a strain-preserving network flow model." #Bioinformatics #rustlang github.com/bluenote-1577/…

"We propose a dynamic bit vector structure that draws a parallel with Elias-Fano's scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression" 👏👏👏 #Bioinformatics github.com/imartayan/CBL