New work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

@lfeatherstone.bsky.social and I have just released v1.10.2 of clockor2.github.io 🎉 including several performance upgrades. Here we reproduce the results of McBride et al 2023, showing accelerated evolution of SARS-CoV-2 in white-tailed deer transmission clusters 🦌🦠 go.unimelb.edu.au/ydo2

Thank you very much to the folks at Seqera for the opportunity to speak about new adventures in Bactopia. Haha you'll have to wait for the video for the jokes, but for now the slides are available here: bactopia.io/impact-and-o...

New feature for PearTree - root-to-tip plots. Web version at peartree.live | desktop apps to follow at github.com/artic-network/peartree/releases/latest

Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....

Wow, this is amazing @wytamma.bsky.social!

At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa.... It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍

Very happy to see Wasm gaining traction as a low barrier to entry alternative for programming thanks to the massive efforts by @quantstack.bsky.social 🎉 We're collecting Wasm resources for bioinformatics and beyond at wasmodic.github.io

Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁

I made a map of 3.4 million Bluesky users - see if you can find yourself! bluesky-map.theo.io I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

Herple 1001 2/5 🦎🦎🦎🦎🦎🦎 🦎🐸🐸🐸🐸🦎 🦎🦎🦎🦎🐸🦎 🦎🐸🐸🐸🐸🦎 🦎🐸🦎🦎🦎🦎 🦎🐸🐸🐸🐸🦎 🦎🦎🦎🦎🦎🦎 herple.wytamma.com

I made this over the break. Why would I do such a thing? Am I some sort of #phylogenetics dork? Well... yes, but that's not why. To fully explain I'll have to do one of those sewing-strings-wrapped-around-a-spool dealies. 1/ 🧪

🚀 Just launched: GraphBin Visualise (WASM) a browser-based visualisation tool for comparing initial metagenomic binning results vs refined results from GraphBin - all running in your browser, no backend required. (1/n) #bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly

Workshop landing page with demos here -> wasmodic.github.io

This was one of the best workshops I have ever been to. I came out of it with a Wasm app for making pharokka/phold/phynteny's genome maps - available at gbouras13.github.io/phold-plot-w... It runs the browser almost instantly - please give it a go with your phages of interest! #ABACBS2025

Woot! The mim preprint is live now. www.biorxiv.org/content/10.1... Happy Thanksgiving! Cc @curiouscoding.nl

Client-side bioinformatics workshop done ✅ massive thanks to legends @lonsbio.bsky.social @lfeatherstone.bsky.social @torstenseemann.bsky.social #ABACBS2025

Loved hearing from Dr. Wytamma Wirth about a deep learning approach to bacterial taxonomic clasification, BABET. The coolest part for me was hearing how tiny the database is! #ABACBS2025 ⚫️🔴 🔵⚪️

Grateful to #COMBINE2025 and #ABCABS2025 for the opportunity to present my PhD work. Always inspiring to meet people who are as excited about your research as you are 😅

It's not just because @torstenseemann.bsky.social is a bioinformatics legend but this may be my favourite #abacbs2025 poster because I'm a #trek tragic 🖖

@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

Wytamma Wirth from @thedohertyinst.bsky.social speaking about a new deep learning approach to bacterial taxonomic classification

Sci-nonfi

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

Great work team!!

Your #MicroSeq2025 committee - @mozztacular.bsky.social , Asad Prodhan, @royalfizzbin.bsky.social , Mozammel Hoque, @wytamma.bsky.social , Rebecca Roach, and @rhyshparry.bsky.social - are all here and ready to go! 🫡 Please feel free to reach out to any of us w/ questions or concerns at any time ♥️

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...

Howdy! I'm currently writing up version 4 of Bactopia! Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link: github.com/bactopia/bac...

We are delighted to announce our plenary speakers for #MicroSeq2025! Dr Rose Collis, Dr Jackie Mahar, Dr Peter Mee, and Dr Leah Roberts! We’ll be treated to four excellent talks across September 3-4. We can’t wait! Register below👇 trybooking.com/events/landing/1424679

🏆 #MicroSeq2025 has plenty of awards on offer! 💰 Cash prizes for best talks are sponsored by @aussocmic.bsky.social, @ausvirologysoc.bsky.social, and #MGen. Plus, loads of merch on offer for the best question of each session! 🖊️📔 Register to submit an abstract👇 trybooking.com/events/landing/1424679

VIPERA v1.2.2 is out!! 🐍 now you can swap in different stats (useful for non-linear allele freq trends). also: new Docker images on release, containerized CI, updated envs, and minor bug fixes for smoother, reproducible intra-patient SARS-CoV-2 analyses 🧪👉 github.com/PathoGenOmics-Lab/VIPERA

Our study on SARS-CoV-2 dynamics and long COVID in Nepal has made it to preprint 🎉 Huge thanks everyone from BNMT, Center for Molecular Dynamics Nepal (CMDN), and the Centre for Pathogen Genomics at The Peter Doherty Institute for Infection and Immunity 👏👏👏 www.medrxiv.org/content/10.1...

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

🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟 #MicroSeq2025

BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be... Details and instructions for installing on the BEAST website: beast.community

Only the fourth case of ABLV in humans. Although ABLV is classified as a different species to rabies virus, the disease is more of less rabies: www.health.nsw.gov.au/news/Pages/2...

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV. These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response. 1/4

Please move genomes to an open pathogen platform like pathoplexus.org!

Hello binfies 👋! There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social. jobs.quadram.ac.uk/Details.asp?...

Prompt injection is a feature not a bug

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again! forms.gle/YJP6WQjsk8KK...

How much did this bad boy cost to make? Like low 10s of millions?

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here: rrwick.github.io/2025/02/07/d...

Introducing SciScroller 🔬 - it’s like TikTok for open scientific papers -> sciscroller.wytamma.com

In the closing hours of the Anna’s Archive $10,000 dollar challenge there are a bunch of submissions rolling in. My favourite is Hypha A‘s Gilbert curve 🔥 -> archive.anarchy.cool/maps/isbn.html

I often have to concatenate a bunch of text files together so I made this `dag and drop` app to streamline the process 📄📄📄➡️📄 - cat.wytamma.com

Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets. www.microbiologyresearch.org/content/jour... (1/4)

What’s your Saturday playlist?