Day 11: A clever bit-counting loop using the "clear bottom bit" trick. Change one compiler flag and... wait, what just happened to my loop?! Pattern recognition at its finest. xania.org/202512/11-po... youtu.be/Hu0vu1tpZnc #AoCO2025

in case you were looking to sponsor cool rust contributors, there is a list now :> blog.rust-lang.org/2025/12/08/m...

I’m recruiting a postdoc to work on algorithms for cancer genome reconstruction. We have access to a rich set of tumour samples sequenced across multiple technologies. If interested, feel free to DM. Please share.

If you ever need to fuzzy search some DNA, sassy is your tool. Please spread the word; I think many people just outside my own circle could benefit from this :) cc @rickbitloo.bsky.social github.com/RagnarGrootK...

The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/

Registration and abstract submission for DSB 2026 is open now! Don't miss your chance to travel to Venice Feb 18-19, which exactly follows the famous Carnival. dsb-meeting.github.io/DSB2026/

A new permutation appeared! My screenname will remain "Ragnar {Groot Koerkamp}" until citations improve.

This double helix is not double helixing correctly.

🧬Explore the latest from Bioinformatics Advances: “Ish: SIMD and GPU accelerated local and semi-global alignment as a CLI filtering tool.”   Read the full paper here: https://doi.org/10.1093/bioadv/vbaf292 Author: @ducktapeprogrammer.bsky.social

In other news, it took some time, but I'm finally starting a postdoc in Peter Sanders' Algorithm Engineering group at KIT (Karlsruhe)! You'll get everything you're used to, plus new theoretical analyses of fast fundamental data structures :)

We developed <new tool> in <language that I don't see being used>, using only the standard library to ensure portability.

"Prolonged exposure in shared, poorly ventilated spaces… drives respiratory virus transmission more than close contact." www.nature.com/articles/s41...

And if you have a .fastq.gz.mim already present, you get another up to 2x speedup (or more with >6 cores).

Code review: do you know why this code triggers undefined behavior? play.rust-lang.org/?version=st...

TIL Deacon decompresses fastq.gz 3x faster than GNU coreutils gzip/zcat. You can decompress, dehost and recompress fastq.gz using Deacon in less time than only decompressing using coreutils gzip/zcat or pigz.

1/9 Just out: k-mer indexes are the backbone of fast search in genomic data, but many degrade under small k, subsampling, or high diversity. With Ondřej Sladký and @pavelvesely.bsky.social we asked: can we build one that works efficiently for any k-mer set?

We now have a working proof-of-concept implementation of the mim-enabled fastq parser in Rust. It uses needletail for the actual parsing and is *already* ~30% faster than the C++ implementation! Very excited about where this will go! cc @curiouscoding.nl

Preprint Alert! We present new strategies to accelerate large-scale document comparison using MinHash-like sketches. A thread:

Are you minimizer-curious yet?

Preprint alert! We introduce new ideas to revisit the notion of sampling with window guarantees, also known as minimizers. A thread:

Oh yes, it is definitely happening for reviews, I am sure for one of the reviews of my last paper - the long rambly summary of the entire paper, emphasising minor things. But at proof stage it is particularly annoying to have many edits, often wrong, but no track-changes.

Postdoc and PhD positions in combinatorial optimization and/or TCS at Lund University. Application deadline January 16. Postdoc position info at jakobnordstrom.se/openings/Pos... and PhD info at jakobnordstrom.se/openings/PhD....

Ready for #NWERC!

I'm continuously impressed with how just how good the Rust ecosystem is. Whenever I look for a crate or a CLI utility that does what I want, 95% of the time I find it. And the rest of the time, the components are right there for me to build it.

mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1

Woot! The mim preprint is live now. www.biorxiv.org/content/10.1... Happy Thanksgiving! Cc @curiouscoding.nl

Okay, #SeqBim is over, let's get crackin' and speak about our recent preprint (joint work with @imartayan.bsky.social, Lucas Robidou, @camillemrcht.bsky.social and @npmalfoy.bsky.social) 1/

We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...). You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.

Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1

I for one welcome the new laptop-benchmarked search tools. Stuff like this enables previously difficult or impossible study under independent research contexts. For example, my warehouse lab's grid's so terrible running all threads on the main workstation trips the circuit breaker. 🧬💻

see this is what I meant re: facet's direction. if I'm not trying to make the tiniest lib ever I'm free to make it have the best DX/UX

Ok — here's the current version of the mim preprint: bit.ly/4pygyyc! Hopefully it will make it to @biorxivpreprint.bsky.social soon, but who knows with the holiday week. Anyway, by the time it hits, we'll probably already have interesting updates to share. Happy to answer questions :).

The Cloudflare front for biorxiv is just completely broken for me at this point. Can't open anything on mobile anymore.

Minimizer Density revisited: Models and Multiminimizers https://www.biorxiv.org/content/10.1101/2025.11.21.689688v1

You know, we’ve got a saying

I'll be in Cambridge first half of next week and Oxford second half! Hit me up if you wanna hang out :)

And when you're trying to write an elite Rust implementation of something, who do you want on board? That's right! I was lucky enough to convince @curiouscoding.nl to join the mim team!

OH. MY. GOD. TYPST IS SO SMOOOOOTHHH. 100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update. Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).

Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2

"the camera is 400 megapixels" every photograph takes up 300 MB just to take 8 out of focus pics at a time of a dog being cute and the one posted will be seen 3 inches wide on phone screens or facebook feed by people who know the dog and say "aw look at sparky" you're trying to selling cloud storage

Once upon a time there was a dude. He thought 3ns is slow, since time=$$$. After a year of hard work, he got it down to 2ns. Then he tried it on a .gz file, and realized it takes 25ns. All his effort was in vain. Today, we remember the friends [assembly instructions] he made along the way.

- CEO [2 person company] - manager [10 reports] - prof [25 people lab]

using AI for code is great to get you 50% of the way there, especially if you were 80% there already

Spicy take of the day: YAML is not *that* bad. (If you're the one writing it) (And the one deserializing it) (And you can use json-schema for validation in your editor)

Sure, yeah, of course. I still don't understand why clicking, like switching from issues to merge requests on a completely empty instance should take 1.5 seconds and that much RAM. I, you know, I feel like the tech stack being used has more to do with that than the feature set!

Oh my God, GitLab is running on a beefy server literally next door and it feels so sluggish. Oh my God, I don't think I can use this.

In more than decade of writing Rust, I have never once in my life needed back pointers for anything.

even the default slack notification sound just screams sluggishness why give 3 beeps when one does? you had my attention at the first and are now stealing it for another half second

Binding escape (=caps key) in normal-mode to save 🤯

We need XDG_CONFIG_HOME for git repos. Really tired of throwing more and more config files into the root. Imagine if all that would go into `config/`. And then, how about making that a submodule so that whenever you find a new tool, you only need to add configuration once? One can dream :)