ahh, CMake, the best of what 1973 had to offer I'm sure

Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1

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/

github.com/bede/deacon For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️

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

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.

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/

@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2

Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...

The simplex algorithm is super efficient. 80 years of experience says it runs in linear time. Nobody can explain _why_ it is so fast. We invented a new algorithm analysis framework to find out.

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

Movi 2: Fast and Space-Efficient Queries on Pangenomes. #Pangenomes #SequenceQueries #Genomics #Bioinformatics @biorxiv-genomic.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

So what's the equivalent of `perf record && perf report` on a MacBook? I want to see the generated assembly and which lines are hot.

Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ? www.nature.com/articles/d41...

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary." engineering.fb.com/2025/10/06/d...

We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...

#RECOMB2026 is now accepting submissions and we'd love to see your best work! 📌 Abstract registration: Nov 7, 2025 📌 Full paper submission: Nov 14, 2025 📜 More info: recomb.org/recomb2026/call_for_papers.html

🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

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

Looking for people to test the latest version of simd-sketch. It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower). 'cargo install simd-sketch' is right there under your fingertips ;) github.com/RagnarGrootK...

There are millions of openly available microbial genomes, but searching them can be slow. Until now 🥁 Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more. www.ebi.ac.uk/about/news/r... 🦠

Vous pouvez soutenir ma proposition à la Cour des Comptes d'examiner les marchés publics de voyagistes, notamment dans l'ESR : participationcitoyenne.ccomptes.fr/processes/co...

#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!

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

Critical part of the President's new $100,000 charge for H1-B visas: The Administration can also offer a $100,000 discount to any person, company, or industry that it wants. Replacing rules with arbitrary discretion. Want visas? You know who to call and who to flatter.

Minimap2 is very much the hammer in "When all you have is a hammer, everything looks like a nail."

Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

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

A wonderful day for @bonsaiseqbioinfo.bsky.social, with @camillemrcht.bsky.social's and @npmalfoy.bsky.social's HDR defenses. Congrats for the amazing work! It's a great chance for the team to have you both!

We are glad to announce that the next workshop “Data Structures in Bioinformatics” (DSB 2026) will take place in Venice, Italy, on *February 18-19*, 2026. dsb-meeting.github.io/DSB2026/ Book the dates! #DSB26

📣 Deacon 0.8.0 available on Bioconda - Much faster search and depletion through improved work distribution on multicore systems. My fastq.gz benchmark now runs at 400Mbp/s on Apple M1. - Dual default match thresholds for greater accuracy Details: github.com/bede/deacon/... 1k downloads! 🐥

So, the heap I invented over the weekend was introduced as the quickheap by Navarro and Paredes around 2006! Basically: on each pop, do just enough quicksort to find the smallest element. My implementation (the 1st??) is 2x to 4x faster than d-ary and binary heaps. curiouscoding.nl/posts/quickh...

There was a workshop on 25 years of the FM-index and the CSA after SEA. I would have liked to attend, but I had other commitments. The invited speakers were Giovanni Manzini and Roberto Grossi, as the other purpose of the workshop was to present them Festschrifts for their 60th birthdays. 1/6

Little writeup on the speed of fasta parsers, at last. Basically: both needletail and paraseq are process input linearly, and thus have a limit around 4 GB/s. By giving each thread its own slice of the input file, we're limited by RAM bandwidth instead :) curiouscoding.nl/posts/fasta-...

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3

I talk a lot about Rust for building high-perf (& even non-perf critical) software, & scientific software in particular. I often discuss what's interesting to me, but wanted to offer the chance to those interested for me to answer their questions about Rust in science. Fire away with questions!🧬🖥️

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

Slides for PtrHash are here curiouscoding.nl/slides/ptrhash/

Congrats to @curiouscoding.nl for getting the #SEA2025 best paper award for his work on PtrHash! drops.dagstuhl.de/entities/doc...

If you’re in Liverpool, stop by my poster A217 at ISMB/EECB 2025, and chat about all things pangenomes, MUMs, and alignment (and the Beatles or Oasis-mania)

Excited to attend #SEA2025 this week in Venice! I'll present our work on simd-minimizers on Thursday! Meanwhile, you can take a look at the slides here: igor.martayan.org/slides-sea-2...

How well do you know Python’s f-strings? I built a thing inspired by JavaScript’s Date constructor quiz but for Python. fstrings.wtf

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...

Ohhhh, it's proceedings day! Time to update citations for SimdMinimizers, PtrHash, and U-index 🎉 drops.dagstuhl.de/entities/vol...

Finding easy regions for short-read variant calling from pangenome data arxiv.org/abs/2507.03718 🧬🖥️🧪 github.com/lh3/panmask

Maxime Crochemore, Thierry Lecroq, Wojtek Rytter 25 Additional Problems -- Extension to the Book "125 Problems in Text Algorithms" https://arxiv.org/abs/2507.05770

All Bonsai related communications during #JOBIM2025. Come meet us 👇🏻

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...