Give a toy to a cool kid, he'll break it but he'll think of ways to fix it too. Check Igor's blog post on ntHash.

New blog post!

I use ntHash all the time to hash k-mers, yet it turns out it has some unexpected flaws (collision propagation, bias on leading zeros...). The good news: each of them can be fixed!

igor.martayan.org/posts/breaki...

An Earthshaking Announcement YouTube video by River Valley Technologies

Every time I see you write Fulgor with the ⚡, I think about Knuth's iTeX (youtu.be/eKaI78K_rgA?...) 😂

Ditto; on both counts. I still have an old e-mail of @mikeschatz.bsky.social giving me feedback on an assignment in a class taught by @stevensalzberg.bsky.social. Now, both Mike and Adam are computational genomics legends! As, of course, are you, Ben!

Amazing work, as always, from @ale-campa.bsky.social! Now you can index AllTheBacteria v2 (sans dustbin and unknown) in only 130G. It’s always a pleasure to work with @jermp.bsky.social and @ale-campa.bsky.social, and I’m very excited for where Fulgor is going next!

Really proud of @ale-campa.bsky.social for his amazing contributions to the Fulgor ⚡ index! I'm very excited for what's next 🙂 CC @robp.bsky.social @zaminiqbal.bsky.social

I don't consider my own libraries that I've rewritten in Rust to be competing. They are either replacements, or parallel versions. If the rewriter is different from the original dev, it's great if the original dev is involved, but IMO that's not essential to add value.

As an algorithmic bioinfo dev myself, I do feel that Rust provides a clear benefit for many tools in the space (mostly CLI tools). As @lh3lh3.bsky.social points out, there are very real benefits for having the tool written in Rust, rather than just having Rust bindings. lh3.github.io/2026/04/17/t...

Glad I just added support for plex technologies to alevin-fry ;P.

That said, I do have many reservations about the rewrite approach. Specifically, the velocity and, maintainence questions & #of concurrent projects *not* reaching usable status. I think there can be real added value to a true rewrite, but I think we should find a good way to do this. 2/2

The purpose of this project (not mine) is explicitly to avoid bindings. Honestly, I see the value of real ports, and have written some of my own software (and one, for fun example of WFA-lib). Relying on FFI makes the build process harder, opens more safety bugs, & can degrade perf. 1/2

Finally, I also am in favor of disclosure of AI written code (and think the commit messages and other notes are a reasonable way to approach it for now). However, this is just a preference that I have (for several reasons), and the code has the quality it does, regardless of the author... 3/3

Several (though not all) of the repos have caveats about completeness / expectations. On one hand, I absolutely see the potential for bad outcomes, & retain a healthy skepticism. OTOH, I want to give folks the benefit of the doubt, and see openness and discussion moving in the right direction. 2/3

GitHub - henriksson-lab/rustification Contribute to henriksson-lab/rustification development by creating an account on GitHub.

To be clear, I don't think that the README suddenly makes it great, but I think it provides useful information. The person/lab doing all of these rewrites also has a statement on the motivation and method : github.com/henriksson-l...

I think that sustainability & pace are very real questions. 1/3

Nice! Can we get a pic? ;P

Don't port without support!!

“Bioinformatics would be a more enjoyable field if more tools were written in Rust.”

Shout it from the rooftops

QCatch: A framework for quality control assessment and analysis of single-cell sequencing data AbstractMotivation. Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstrea

QCatch is now published in Bioinformatics (academic.oup.com/bioinformati...)! Great work from Yuan and Dongze for quality control and analysis downstream of simpleaf/alevin-fry (taking advantage of its structured AnnData output). Give it a try: github.com/COMBINE-lab/...

Announcing Rust 1.95.0 | Rust Blog Empowering everyone to build reliable and efficient software.

Rust 1.95!

* IF-LET GUARDS; LFG!!!!
* compile-time `cfg_select!`
* a bunch of stabilizations

blog.rust-lang.org/2026/04/16/R...

Ok, so now there's a document that's laying things out a bit more cleanly. I still have a lot of thoughts, but it's useful to understand the motivation and the goals here. Also, the document itself seems to have reasonable first principles: github.com/henriksson-l...

New lab server is accessible! Now, I have to decide on the drive/volume layout. I'm working with ~92TB of NVMe gen5 storage. Any suggestions on setups for such storage that has worked well for folks in the past?

How about calling it "The Best Lab (whose PI is not Dr. Best)".

Computeral Bioinfology is the root discipline. It undergirds both bioinformatics and computational biology, as well as computational genomics and, in fact, reality itself!

@pashadag.bsky.social : the LG is pretty sweet so far!

updates to piscem -> alevin-fry -> simpleaf incoming! Much faster probe based quant with *identical* results to prior versions. 2/2

Massive thanks to @jacksonweir.bsky.social for sharing some 10x Flex v2 data! Not only did it help us solve a latent bug(10x whitelist is reverse complemented), but led to a new special index for probe-based quant. I just quantified 2.3B flex v2 reads on my laptop CPU in 32 minutes! 1/2

And we couldn't even get the name mim...

With the heavy discounting on the first year of .bio domains right now, how can we not? It is decidedly not well-considered, but I will accept debate only in the form of a pull request

compbiovs.bio

Looks very cool, but name collision! link.springer.com/article/10.1...

The resolution is important IMO for sharp text. Contrast maybe less so. However the large physical size on a single monitor is a real win. What is sway? At work I use it on Cosmic Desktop with their built in tilin manager. It works well.