New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)

Honoured to be awarded the Mary Lyon medal by the Genetics Society today, here in Edinburgh. V grateful to mentors and all my previous group members and colleagues. Medal is an X chromosome!!

Genetics Society UK@gensocuk.bsky.social · last mo.

Congratulations to Prof @zaminiqbal.bsky.social, recipient of the 2026 Mary Lyon Medal, on delivering an inspiring lecture at Genetics Society Anniversary Day 2026 in Edinburgh.

I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets. More info globdb.org 🦠🖥️🧬

2/2 ESA-E accepted: - SimdQuickHeap [w/ Johannes Breitling, Marvin Williams] - non-minimal k-PHF [Stefan Hermann, Peter Sanders, Stefan Walzer] and 2/2 WABI accepted: - O(n lg lg n) chaining [Nicola Rizzo] - anti-lex SUS-anchors arxiv: arxiv.org/search/?quer...

Ragnar {Groot Koerkamp}@curiouscoding.nl · last mo.

And ESA 🤞

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

Just a shout-out to the folks over at @pathoplexus.org and, importantly, all the scientists sharing genomic data with such amazing speed. It's great to see the field having moved to a new platform, with non-transparent platforms being a thing of the past. Fantastic.

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...

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

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!

LexicMap v0.9.0 has been released with - a few bug fixes: CIGAR, bitscore and evalue calculation. - new features: better support for big genomes like human. - a new command to convert output to SAM format github.com/shenwei356/L...

Release LexicMap v0.9.0 · shenwei356/LexicMap

v0.9.0 - 2026-03-13 New commands: lexicmap utils 2sam: Convert the default search output to SAM format (#26). Attention: This command requires search results generated by the current LexicMap ver...

github.com

Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! I'll keep maintaining it. github.com/shenwei356/s...

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit

Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

github.com

I should have said, this takes us to about 2.8 million genomes in total. We don't have annotations, etc for the latest data yet, this will be an ongoing process

Zamin Iqbal@zaminiqbal.bsky.social · 5mo ago

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

nature.com

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Protein structure-informed bacteriophage genome annotation with Phold

Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.

academic.oup.com

George Bouras@gbouras13.bsky.social · 12mo ago

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

For those of us interested in software development, data structure design etc in science, this is a must-read. A taste of what is happening in communities letting AI agents go wild writing code, creating PRs, writing documentation : spoiler - humans get addicted, lose perspective, slop everywhere.

Armin Ronacher@mitsuhiko.at · 7mo ago

Weekend thoughts on Gas Town, Beads, slop AI browsers, and AI-generated PRs flooding overwhelmed maintainers. I don't think we're ready for our new powers we're wielding. lucumr.pocoo.org/2026/1/18/ag...

Phage therapy of perinephric abscess in kidney transplantation recipients caused by drug‐resistant Pseudomonas aeruginosa - Liu - 2025 - mLife - Wiley Online Library onlinelibrary.wiley.com/doi/10.1002/...

Phage therapy of perinephric abscess in kidney transplantation recipients caused by drug‐resistant Pseudomonas aeruginosa

Click on the article title to read more.

onlinelibrary.wiley.com

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

nature.com

My first Rust toy tool (just for learning purposes)!!! The performance (both time and memory) is good! Rust is hard to learn, and I still need more practice! github.com/shenwei356/f...

Most exciting study have seen for ages, and Fernando the most excited speaker. Much anticipated. Highly recommended, a lot of food for thought (and quite a dense paper - lots to think about)

Michael Baym@baym.lol · 9mo ago

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

It's Monday! ...and a new #MVIF program is out! 🤩 Free registration: cassyni.com/s/mvif-44 ⭐️ Highlights: 🇺🇸 Vanessa Hale 🇰🇷 Jun Hyung Cha ⭐️ Keynote: 🇺🇸 Katherine Lemon @kathlemon.bsky.social ⭐️ Talks: 🇺🇸 Meenakshi Chakraborty 🇨🇳 Wei Shen @shenwei356.bsky.social 🇺🇸 Johanna Gutleben

📣 New preprint from us at phagefoundry.org 📣 A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort www.biorxiv.org/content/10.1...

Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.

Genetics Society UK@gensocuk.bsky.social · 9mo ago

Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!

Our method for genome size estimation from long-read overlaps is now published 🥳 academic.oup.com/bioinformati...

Genome size estimation from long read overlaps

AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin

academic.oup.com

Thread on #GI2025 's second day! 👇🏻

Sina Majidian@sinamajidian.bsky.social · 9mo ago

Second day of Genome Informatics #GI2025 began with the session “Genome Assembly and Sequence Algorithms" Yun William Yu presented “Average-case Analysis of Seed-Chain-Extend under Random Mutations" genome.cshlp.org/content/33/7/1175 providing theoretical guarantees for the popular seed-chain-extend

Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory. List of talks and posters: meetings.cshl.edu/abstracts.as...

Cool paper new paper from Lorién López-Villellas, @santiagomarco.bsky.social and others! Super cute and simple idea: In Gotoh's affine-cost alignment, only the M matrix is needed during tracing: we can just search for a gap-length x such that M[i][j] = M[i-x][j]+o+x*e or M[i][j] = M[i][j-x]+o+x*e.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 9mo ago

Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment https://www.biorxiv.org/content/10.1101/2025.10.31.685625v1

I also have serious concerns about the consolidation of roles (one person is now publisher, chief editor, and also a frequent author) as exemplified in a recent paper that was fast-tracked for publication.

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.

Rick Beeloo@rickbitloo.bsky.social · 10mo ago

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...