miniSNP (minisnp.wytamma.com) is a fun/educational microbial variant caller that lets you watch your reads mapping and variant calling in real-time 🚀 🦠 📊 I hope this is helpful for people trying to learn or explain read mapping and variant calling!
Wytamma
@wytamma.bsky.social
Enjoying the little things like antibodies, ion channels and pip installs - technical biologist building tools and studying diseases ❤️🐢
One of the reasons I'm interested in local AI models is you're data can't be used for training - people say “I already put my data in onedrive so what's the difference to uploading it to an AI model?” Well one difference is that onedrive won't use your data to scoop you
Carl Zimmer@carlzimmer.com · 2w agoFour days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences! Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses. 📰 Read more: pathoplexus.org/news/2026-09...
Great to see more recognition for the hard working binfies ❤️ Well done Dan!
MicroSeq2026@microseqasm.bsky.social · last mo.The #MicroSeq2026 Innovation in Bioinformatics Award goes to Daniel McKnight, who presented an automated pipeline for molecular diagnostic assay design and evaluation! Our field depends on creative, innovative minds like yours. Congratulations Daniel! #MicroSeq2026
Until next year, @royalfizzbin.bsky.social, @wytamma.bsky.social, @mozztacular.bsky.social, Asad, Mozammel, @bioelogy.bsky.social, and Clara out!
✨ We hear you! Due to popular request, the deadline to submit an abstract to #MicroSeq2026 has been extended ONE MORE WEEK! 🚨 NEW DEADLINE (and this one's final): 11:59PM, Friday, August 7, 2026 🚨 Don't miss out! Register and get your abstracts in here 👉 trybooking.com/DNRBW
Check out our new Makefile tutorial if you want to finally understand what those "make install" commands actually do when you paste them in your terminal, and how to use them in your work: sandbox.bio/tutorials/ma... Thanks to Stephen J Bush for contributing this tutorial!
Intro to Makefiles
Interactive make tutorial: learn to use and create your own Makefile using a command-line interface in your browser.
sandbox.bio
Clockor2 v1.12.1 adds date-randomisation tests 🎉 Date randomisation is a permutation test for temporal signal: does the observed relationship between sampling time and genetic divergence exceed what we would expect if dates were unrelated to sequences?
📣Calling Australian/NZ ECRs and PhD Students 📣 Abstract submission and registration for #MicroSeq2026 opens July 6! Abstracts for both medium-length and lightning talks will be welcome.
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
Sam Horsfield@samuelhorsfield.bsky.social · 5mo agoOur 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...
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...
Presentations | Bactopia
A curated Collection of Bactopia related Talks and Posters.
bactopia.io
Nextflow@nextflow.io · 6mo ago🦠 Avoiding AI slop in Bactopia! Robert Petit from Wyoming Public Health Laboratory is back to share how they took a directed approach to AI coding, building coaching guides, documentation for LLMs, and an "add-tool" skill that lets users contribute new tools to the pipeline. #NextflowSummit
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....
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
github.com
Wow, this is amazing @wytamma.bsky.social!
Wytamma@wytamma.bsky.social · 7mo agoAt 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 ❤️ 🐍
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 ❤️ 🐍
snakemake.github.io
Johannes Köster@johanneskoester.bsky.social · 7mo agoToday, the #SnakemakeHackathon2026 at the TU Munich ended with the release of Snakemake 9.17! I want to thank all participants and my co-organizers! You have been incredibly dedicated and we improved a ton of things throughout the ecosystem.
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
wasmodic.github.io
Zamin Iqbal@zaminiqbal.bsky.social · 8mo ago@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n
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 😁
EMBL-EBI@ebi.embl.org · 8mo agoThe AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities. This includes rich datasets for microbes, viruses & parasites associated with tropical diseases. Explore the new datasets in the AlphaFold Database. www.ebi.ac.uk/about/news/u...
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
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
bluesky-map.theo.io
Herple 1001 2/5 🦎🦎🦎🦎🦎🦎 🦎🐸🐸🐸🐸🦎 🦎🦎🦎🦎🐸🦎 🦎🐸🐸🐸🐸🦎 🦎🐸🦎🦎🦎🦎 🦎🐸🐸🐸🐸🦎 🦎🦎🦎🦎🦎🦎 herple.wytamma.com
Herple - Wordle for lizard people
Wordle for lizard people.
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
GitHub - metagentools/graphbin-visualise-wasm-app: GraphBin Visualise WebAssembly App
GraphBin Visualise WebAssembly App. Contribute to metagentools/graphbin-visualise-wasm-app development by creating an account on GitHub.
github.com
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
phold_plots — Pyodide
gbouras13.github.io
Wytamma@wytamma.bsky.social · 11mo agoClient-side bioinformatics workshop done ✅ massive thanks to legends @lonsbio.bsky.social @lfeatherstone.bsky.social @torstenseemann.bsky.social #ABACBS2025
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1... Happy Thanksgiving! Cc @curiouscoding.nl
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compr...
biorxiv.org
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 🖖
