Min-frame transformation enables more sensitive viral genome alignment https://www.biorxiv.org/content/10.64898/2026.05.20.726535v1

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.

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...

what's the current status of HERRO and (bacterial) nanopore? Last I saw was Ryan Wick's blog evaluating it. How many people now use it (or did it actually get folded into a basecaller, or did it get dropped in favour of something else)?

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

📌 Les #soumissions pour @jobim2026.bsky.social sont ouvertes jusqu'au 15/03/26. 📝 Soumission de travaux originaux, articles longs (+ PCI), activités de plateformes et de service, posters et démonstrations 📍 Plus d’infos sur : jobim2026.sfbi.fr #JOBIM2026 #bioinfo #Strasbourg

🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup. libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix github.com/ebiggers/lib...

"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from @martinsteinegger.bsky.social andco

Inverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1

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/

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?

Preprint out! Check out our new long-read metagenomic SNP-caller, SNooPy 😀. Work with Chris Quince. Thread 🧵 👉 www.biorxiv.org/content/10.6...

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

Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6) 👉 Preprint www.biorxiv.org/content/10.1... 👉 Github github.com/rolandfaure/...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification. 🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1 1/9

Starting #RECOMBseq with @rayanchikhi.bsky.social 's keynote. Here stressing our responsibility as scientists to enable access to a common good: genomic data

Side note: you could, speaking purely theoretically, also fit every microbe onto an SD card, which is within the weight limit for a carrier pigeon. For some distances, it would be faster than the internet for transmitting sequence libraries 7/

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

So glad to have participated in #DSB2025, what a great workshop! For some mysterious reason it was the first time I attended after 3 years of sequence research. Thanks to all participants & organizers 😃

Ragnar's made some incredible optimizations on the computation of minimizers, can't wait to see how these improvements will benefit bioinfo tools!

Amazing ideas here www.biorxiv.org/content/bior... from @yoann.bsky.social and collaborators. Reorganize minimizers to allow kmers dichotomic search. That's brilliant. #bioinformatics 🧬🖥️

So glad to have successfully defended my Ph.D. last week 😀 Work on producing haplotype-resolved metagenomic assemblies using noisy long reads (HairSplitter) and high-fidelity long reads (Alice assembler, unpublished yet). Thanks to my advisors Dominique Lavenier and Jean-François Flot ❤️