Happy to see that K2Rmini was recommended today by PCI Mathematical & Computational Biology. "quickly evaluate whether an arbitrary sequence has a number of k-mer [of interest] matches above or below a threshold." by @imartayan.bsky.social and colleagues: www.biorxiv.org/content/10.1...

Does your designed active site already exist in nature? Is an uncharacterized protein hiding a catalytic site or a pocket? Folddisco answers both, searching millions of structures for a 3D motif in seconds. @natbiotech.nature.com 🧬 📄 www.nature.com/articles/s41... 🧵1/7👇

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

Glad to announce that our new long-read metagenomic SNP caller, SNooPy, is published in NAR! Existing long-read SNP callers are not designed for metagenomic data, check out our new solution 👉https://academic.oup.com/nar/article/54/10/gkag556/8700491 @narjournal.bsky.social

Now also on arxiv arxiv.org/abs/2606.01190

Congrats to @leoackermann.bsky.social on winning RECOMB's best poster award for his work on compressing pairwise distance matrices! Check it out here: lacker.gitlab.io/pdf/research...

Memory-safe high-performance sequence mapping with rammap https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1

Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1

Is anyone attending #RECOMB2026 with a talk in the Sequencing 2 session who would be willing to switch slots with a talk in Sequencing 1 a day earlier? We’d be very grateful. Please reach out if you might be willing to do this!

More and better human assemblies. Now annotate them to the minute. Special kudos @trhyker.bsky.social @jnalanko.bsky.social and @florisbarthel.bsky.social

Rivers of France. #rayshader adventures, an #rstats tale

wow — the preprint host, arxiv, is banning authors for a year if they submit papers with hallucinated citations 🤖

Me in group meeting update: Sassy was accepted at Bioinformatics, and Barbell should be accepted soon. Me at end of group meeting update: Both Sassy and Barbell are now accepted at Bioinformatics 🎉 Who will be the first to cite? All thanks to the wonderful work of @rickbitloo.bsky.social!!!

🔍 New paper in Bioinformatics Advances: "Kaminari: A frugal colored index for approximate k-mer queries"  Read it here: https://doi.org/10.1093/bioadv/vbag120 Authors include: @yhhshb.bsky.social, @yoann.bsky.social, @robp.bsky.social, @pierrepeterlongo.bsky.social, @jermp.bsky.social

This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.

The RECOMB-Seq 2026 program is now available! Join us May 24–25 in Thessaloniki, Greece, for two days of cutting-edge biological sequence analysis, with keynotes by Camille Marchet (CNRS) and Manolis Kellis (MIT). Full schedule: recomb-seq.github.io/seq2026/prog... #RECOMBseq

New preprint: The SimdQuickHeap is the fastest priority queue by far! 2x faster than a radix heap and up to 10x faster than binary heaps. arxiv.org/abs/2604.25681 with Marvin Williams and Johannes Breitling:

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...

Turns out that the usual NtHash is not as random as one might think?!?! At least not for minimizers. Seq-hash (and simd-minimizers) already has this fixed by default ;) github.com/rust-seq/seq...

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...

The fastest way to match characters on ARM processors? https://lemire.me/blog/2026/04/19/the-fastest-way-to-match-characters-on-arm-processors/

I think this blog post comes closest to my current thinking on AI than any other I've read: fransskarman.com/im_not_using...

I'm not looking forward to a future where all the tools are being vibe-rewritten into languages people don't want to learn. Who will maintain all this? The original maintainers won't. It's not the language they were comfortable with. Does the prompter understand the tool well enough?

I kept being rate limited by doi2bib, so I made a small CLI to replace it locally: github.com/imartayan/bi... It can output bibtex from DOIs and arxiv/biorxiv links, redirect to the published version when it's available and copy the result to your clipboard

Modern DRAM is based on a brilliant design from IBM. But, we're still paying for a latency penalty that's existed since the 60s! In this video, I'm introducing my research project (Tailslayer) that immensely reduces p99.99 latency on traditional RAM!

Yeah; I have a bunch of incoherent thoughts about this... 1) maintaining bindings is annoying and purely a service. I already have the rust code and don't need bindings myself. 2) somebody needs to own them. Typically the main dev (me), even though someone else is the user and expert. (1/10)

A quick rant on people vibe-translating our Rust libraries to other languages That's the second time in a week that I see new bioinformatics tools with a vibe-coded translation of our Rust libraries to C/C++. I have two major issues with that:

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers https://www.biorxiv.org/content/10.64898/2026.03.26.714584v1

Why phylogenies compress so well: combinatorial guarantees under the Infinite Sites Model https://www.biorxiv.org/content/10.64898/2026.03.18.712055v1

Lucas Czech: Fast Iteration of Spaced k-mers https://arxiv.org/abs/2603.25417 https://arxiv.org/pdf/2603.25417 https://arxiv.org/html/2603.25417

Amazing talk, I didn't know about left-right structures!

Niceee, was waiting for this one, and already used it in a few places 😆 Congrats @imartayan.bsky.social et al :)

Super Bloom: Fast and precise filter for streaming k-mer queries https://www.biorxiv.org/content/10.64898/2026.03.17.712354v1

Kamila Szewczyk, Sven Rahmann: Hecate: A Modular Genomic Compressor https://arxiv.org/abs/2603.15390 https://arxiv.org/pdf/2603.15390 https://arxiv.org/html/2603.15390

Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers https://www.biorxiv.org/content/10.64898/2026.03.13.711249v1

It's a good day when the first item in your feed is your own work :) @rickbitloo.bsky.social was annoyed that scanning reads for all 96 rapid kit barcodes is bottleneck in Barbell, so he made Sassy2: 13x (150bp) to 4.6x (8kbp) faster than v1 by batch-searching patterns, and >100Gbp/s on 16 threads!

⏰ Last chance! Register your submission with a placeholder abstract for #RECOMBSeq TODAY. Final paper due March 15, 2026, 23:59 AoE Submit now 👉 recomb-seq.github.io/seq2026/call...

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result

I got nerd-sniped into writing some code for Customizable Contraction Hierarchies, which is an insanely cool and super simple data structure for fast route planning. Nice survey paper by Michael Zündorf et al: arxiv.org/abs/2502.10519 My unpolished implementation nodes: curiouscoding.nl/posts/cch/

Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size. Demo: bede.im/deacon

I had the occasion of presenting nice results about the detection of biological events in De Bruijn Graph at #DSB2026, in the context of my PhD work on #Vizitig ! Thanks to the organizers and colleagues for this amazing and super-inspiring event (and @camillemrcht.bsky.social for the picture).

kache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations https://www.biorxiv.org/content/10.64898/2026.02.13.705625v1

🚨UPCOMING DEADLINES🚨 RECOMB-CG: 13 February RECOMB-RSG: 15 February RECOMB-Privacy: 9 March RECOMB-Seq: 12 March (abstract registration) RECOMB-Arch: 12 March (abstract registration) RECOMB-Genetics: 13 March #RECOMB2026 #deadlines

Preprint alert! arxiv.org/abs/2602.03525 TLDR: ZOR filters are STATIC filters with false positives. -Almost memory optimal: <1% overhead over the theoretical lower bound (!!!) -Fast queries: ~100 ns -Construction cannot fail A thread:

So anyway: BiRank & QuadRank: single-cache-miss rank queries that are double the throughput of other Rust crates and fully saturate the memory bandwidth. Side effect: QuadFm is smaller and 2-4x faster than the next-best FM-index. github.com/RagnarGrootK... raw.githubusercontent.com/RagnarGrootK...

Cool paper on representing a collection of sets via a spanning tree of their differences. This builds upon work by Bookstein ('91 )! as well as work we did in using this representation to compress color sets in Mantis MST. I think this repr. has many important applications! arxiv.org/pdf/2601.23240

Generating minimum-density minimizers https://www.biorxiv.org/content/10.64898/2026.01.25.701585v1

Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster! www.biorxiv.org/content/10.6...

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org