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/

This thread gives really interesting and relevant history!

Kraken 2 (K2) community: we are giving more attention to our new `k2` wrapper, and a NEW functionality since 2.17.0 is: you can build several component K2 indexes, e.g. each covering a different Refseq database, and then query them all at once... github.com/DerrickWood/... 1/6

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

Interested in a post-doc in Israel? The deadline for the Azrieli International Postdoctoral Fellowship is November 19. The fellowship offers generous funding for postdocs to conduct research in any academic discipline at eligible Israeli institutions: azrielifoundation.org/fellows/inte...

Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences" www.biorxiv.org/content/10.1... This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

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/...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching https://www.biorxiv.org/content/10.1101/2025.09.29.679204v1

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date! Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

If you're wondering why we're hosting the pre-print via dropbox, its because arXiv (and bioRxiv) did not accept it (because it is a review). Its a bit disconcerting, because a review is precisely the type of paper that would benefit a lot from pre-publication dissemination and feedback.

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

Excited to share our EvANI benchmarking workflow, published in Briefings in Bioinformatics doi.org/10.1093/bib/... Computing average nucleotide identity (ANI) is neither conceptually nor computationally trivial. Its definition has evolved over years, with different meanings and assumptions (1/5)

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

🌎👩‍🔬 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...

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1... and GH repo: github.com/refresh-bio/...

Sassy: Searching Short DNA Strings in the 2020s https://www.biorxiv.org/content/10.1101/2025.07.22.666207v1

Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏 ‪@rayan.chiki.bsky.social #Bioinformatics

After Tim Hunt won the Nobel, he said, "We do science because we like discovering things about the world...and then boasting about what we found". Any one individual can argue about their own motivation, but it would naive to dispute that's an accurate description of many people.

Paper Alert! Our preprint on the K2R index, being able to efficiently associate kmers to the reads containing them is finally out there! A thread! academic.oup.com/bioinformati...

Paper alert! We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ... TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor! academic.oup.com/bioinformati... A thread!

I worked with Thomas during a three months research visit during his PhD, and it resulted in a paper in NAR. I highly recommend him. doi.org/10.1093/nar/...

Preprint alert! We present K2Rmini, an ultra-fast, grep-like tool that extracts sequences of interest from FASTA/FASTQ files based on their k-mer content. www.biorxiv.org/content/10.1... A thread

🖥️🧬 WABI '25 will not only have excellent keynotes, but an exciting program of papers. The titles and abstracts of all accepted WABI '25 papers are now available on the conference website (wabiconf.github.io/2025/talks/). I'm looking forward to seeing these talks!

🧵1/n Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome? In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.

🚀 We are thrilled to introduce QCatch — a fast, command-line QC reporting tool built for alevin-fry & simpleaf single-cell data! Led by @ygao61.bsky.social & in collaboration with Dongze He 🧬🖥️ . The Preprint 📖 is available at bit.ly/4neSznl. Read more below: 1/3

Preprint alert! 🦌 Our new abundance index, REINDEER2, is out! It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput. Short thread! www.biorxiv.org/content/10.1... github.com/Yohan-Hernan...

Also: what are the bottlenecks in your data processing? Specifically, I'm looking for reasonably well defined & understood and widely used methods that could use a fresh high-throughput implementation. Stuff like sketching, maybe assembly, ... Surely, many pipelines could be sped up 10x ;)

1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

A new preprint on indexing pangenome graphs using an FM-index of the haplotypes and a tag array. Joint work with Parsa Eskandar and @benedictpaten.bsky.social.

@alexanderjpetri.bsky.social's isONclust3 algorithm is now published doi.org/10.1093/bioi.... isONclust3 performs de novo clustering of long-read cDNA sequencing data. A key step in reference-free transcriptome analysis.

The deadline for WABI 2025 has been extended (but is still rapidly approaching) wabiconf.github.io/2025/ * abstract deadline: May 12 (AoE) * paper deadline: May 15 (AoE) Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!

Nice article on (frustrating) life as performance engineer. purplesyringa.moe/blog/why-per...

The list of proceedings papers for #ISMB2025 is up on the website www.iscb.org/ismbeccb2025... ! It's an exciting collection of papers, as always :).

We finally concluded the meeting. Thanks to all attendees for their scientific contributions and for traveling (near or far) to the meeting! Thanks to the local organizers for the infrastructure and catering, and thanks to the co-organizers @yaronorenstein.bsky.social @camillemrcht.bsky.social!

We are hiring PhD students in Computational Mathematics and Mathematics at Stockholm University in various subjects: su.varbi.com/en/what:job/... Application deadline: April 22. (1/3)

PSA: if you are applying to a CS grad program & a faculty member is asking for a verbal commitment before an official offer letter, this is a HUGE 🚩! There is an April 15th resolution to avoid this behavior (cgsnet.org/resources/fo...). I'd urge you to avoid those departments!

Passionate about open science and FAIR data principles for microbiome data? Consider becoming an NMDC Ambassador next year! I was an Ambassador in 2023 and happy to answer any questions about the experience!

🎶 Last Christmas,i gave you m̶y̶ ̶h̶e̶a̶r̶t̶ 40 pages of delicious combinatorics 🎶 Choose any word W of size m. How many words of size k>m admit W as their smallest lexicographical subword of size m ? Find out in my latest preprint!

Over and over again, I come to the conclusion that the process of writing comes down to finding the most intuitive topological order through a high-dimentional space of results. Can be: sort by time, sort by paper, sort by topic, sort by previous work vs new stuff, first simple, then in-depth...

Since indirects are in the news again, and everybody and their dog has an opinion on how much "research overhead" should cost, here's an excellent book that explains where exactly the money goes. escholarship.org/uc/item/59p1...