New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

Automated, almost-error-free consensus #assemblies with Autocycler Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome Once again, incredible, landmark work from @rrwick.bsky.social doi.org/10.1093/bioi... Tool here: github.com/rrwick/Autoc... #bioinformatics #genomics

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

It's Monday! ...and a new #MVIF program is out! 🤩 Free registration: cassyni.com/s/mvif-42 ⭐️ Highlights: 🇦🇺 @gbouras13.bsky.social 🇺🇸 Danica Schmidtke ⭐️ Keynote: 🇺🇸 Peter Turnbaugh ⭐️ Talks: 🇸🇬 Minghao Chia 🇺🇸 @arzamasovalex.bsky.social ‪ 🇳🇿 Brooke Wilson

GPU-accelerated homology search with MMseqs2 | Nature Methods https://www.nature.com/articles/s41592-025-02819-8

Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n) www.biorxiv.org/content/10.1... #Bioinformatics #genomics #assembly #assemblygraphs #software

agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

www.nature.com/articles/s41... #microsky #genomics #phagesky #phage defense

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...

🚨New Review Out🚨 We explore how phage-antibiotic synergy can dismantle efflux-driven resistance in multidrug-resistant ESKAPEE pathogens. By reprogramming bacterial defences, phages offer a precision strategy to restore antibiotic efficacy. journals.asm.org/doi/10.1128/...

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

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

Check out Ryan's new blogpost, especially if you work on and polish small eukaryotic genome assemblies - it's always nice when someone adds new features for your tools

New blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...

🌎👩‍🔬 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: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob #phagesky #microsky journals.asm.org/doi/epub/10....

Thrilled to share our new review just published in Microbiology and Molecular Biology Reviews (@asm.org #MMBR): “Computational Function Prediction of Bacteria and Phage Proteins” with @gbouras13.bsky.social @linsalrob.bsky.social @bedutilh.bsky.social 🔗 journals.asm.org/doi/10.1128/...

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

We're excited to highlight the EMCR Shark Tank 🦈 A new event to be held as part of the ABACBS 2025 Level up your grant pitch & get real-time feedback from leading "Sharks" — with a prize to be won! Details ➜: lnkd.in/gffKiu3h #Bioinformatics #ResearchCareers #EMCR #Grants #ABACBS

🚨 Less than 48 hours left! 🚨 Abstract submissions for #ABACBS2025 close midnight Friday, Aug 15 — no extensions. www.abacbs.org/abacbs2025

After a busy period , @ryancook94.bsky.social and I have have updated links to latest INPHARED dataset. With 37.5K genomes now. If some "iffy" genomes have got thought the automated and then out manual filters. Let us know the accession numbers so we can exclude millardlab.org/bacteriophage-…

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...

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...

🚨 Abstract deadline extended! 🚨 You’ve now got until August 15 to submit for #ABACBS2025 — one-time extension only! Join us in Adelaide for world-class #bioinformatics, workshops, student & EMCR events, and more. 🔗 www.abacbs.org/abacbs2025

MMseqs2 v18 is out - SIMD FW/BW alignment (preprint soon!) - Sub. Mat. λ calculator by Eric Dawson - Faster ARM SW by Alexander Nesterovskiy - MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API) 💾 github.com/soedinglab/M... & 🐍

EOIs to host a workshop at ABACBS 2025 close tomorrow. We've already received a great selection and don't plan to extend the deadline. That said, if you need a little more time reach out via the email in the link below they will try to accommodate www.abacbs.org/abacbs-2025-...

🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages” Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide. 👇 Read on for details! #Phage

🚨 New preprint 🚨 My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky www.biorxiv.org/content/10.1...

Synteny-aware functional annotation of bacteriophage genomes with Phynteny https://www.biorxiv.org/content/10.1101/2025.07.28.667340v1

We have been working on ways to find #phage with long shelf-life and this one is a winner. 12 months freeze-thawing as much as you like, no loss of viability #phageSky #microSky rdcu.be/ewnzT

Really important points by @alexbateman1.bsky.social on the importance of curation, addressing some of the myths out there. Deeply resonates with the commentary Paul Thomas and I wrote last year www.nature.com/articles/s41...

Had a great time at #SMBE2025 presenting our work of bacterial genome classification with AI github.com/bloodhound-d...

New sylph pre-built databases + taxonomy available for: - GTDB-R226 (143k prok. species) - GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social ) - UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social ) Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

Folddisco webserver result view update: - Added description texts for AFDB - Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social - Inter-residue distance clustering by DBSCAN to explore motif diversity. 🌐 search.foldseek.com/folddisco 📄 www.biorxiv.org/content/10.1...

Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins Structural predictions to improve #phage genome annotation! @hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social www.biorxiv.org/content/10.1...

Today at 5pm, @eunbelivable.bsky.social will present her work on the Big Fantastic Viral Database (BFVD) at #ISMB2025 in BOSC. She also has a poster B-123 (tomorrow, 22nd), so please drop by to have ta chat and grab some stickers! 📄 academic.oup.com/nar/article/...

📣 New preprint alert! Happy to share the first results from our effort to reannotate Pseudomonas #phage proteins of unknown function, using structural bioinformatics. 📄 doi.org/10.1101/2025...

🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social. Head to our website to register now 👇 www.microseqconference.com/registration...

My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated): www.k.u-tokyo.ac.jp/en/informati...

📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!

We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB. 💻🧬 #phagesky linsalrob.github.io/PHROG_struct...

Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1

Finally joined Bluesky! Follow along to stay connected with ABACBS. Keep an eye out in the coming days, we’ll be releasing more details for 2025 conference, including opening abstract submissions and announcing invited speakers! www.abacbs.org/abacbs2025

What determines who a phage can infect? We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort. 👇 A thread!

New pre-print alert! 🚨🫁 COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9 www.biorxiv.org/content/10.1...

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at ‪EMBL-EBI (@ebi.embl.org)‬ and the University of Cambridge (@cam.ac.uk‬)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"

Unicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109