Rust for Bioinformatics @rust4bio

The home of the awesome Rust for Bioinformatics community. We are disrupting the status quo! And we love #Bioinformatics and #rustlang 🦀🧬💻❤ Everywhere Joined September 2021

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Rust for Bioinformatics @rust4bio

2 years ago

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

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Zed @zeddotdev

2 years ago

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

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Rust for Bioinformatics @rust4bio

2 years ago

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

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𝕐 @nomad421

2 years ago

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?

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Rust for Bioinformatics @rust4bio

2 years ago

@CamilleMrcht Great, Thanks!

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Rust for Bioinformatics @rust4bio

2 years ago

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

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Rust for Bioinformatics @rust4bio

2 years ago

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

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Igor Martayan 🦋 @IgorMartayan

2 years ago

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…

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Javier Santoyo @jsantoyo

2 years ago

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

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𝕐 @nomad421

2 years ago

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!

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Rust for Bioinformatics @rust4bio

2 years ago

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

Jim Shaw @jim_elevator

2 years ago

We (me and @YunWilliamYu) built a fast coverage calculator for *multi-sample metagenomic binning* called fairy. Available on github (github.com/bluenote-1577/…) and as a short paper on bioRxiv: biorxiv.org/content/10.110… 1/5

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Anicet Ebou @anicetebou

2 years ago

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

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Rust for Bioinformatics @rust4bio

2 years ago

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

𝕐 @nomad421

2 years ago

We had a great meeting & and are moving forward with a GitHub org. for planning & developing foundational building blocks for sequence analysis & related tasks in @rustlang. The org. "rust-seq" can be found here github.com/rust-seq. Reach out if you're interested in joining!

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Naïve Bayesian @naivebayesian

2 years ago

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

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𝕐 @nomad421

2 years ago

#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…

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Vince Buffalo @vsbuffalo

2 years ago

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…

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Vince Buffalo @vsbuffalo

2 years ago

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…

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Rust for Bioinformatics @rust4bio

2 years ago

"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/…

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Rust for Bioinformatics @rust4bio

2 years ago

biorxiv.org/cgi/content/sh…

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Rust for Bioinformatics @rust4bio

2 years ago

"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