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?

I often have to use a metadata sheet to find and replace values in some other files so I made this app to streamline the process 🔎➡️✏️ replace.wytamma.com

Got there in the end! Herple 999 4/5 🦎🦎🦎🦎🦎🦎 🦎🐸🦎🦎🐸🦎 🦎🐸🦎🦎🐸🦎 🦎🐸🐸🐸🐸🦎 🦎🦎🦎🦎🐸🦎 🦎🦎🦎🦎🐸🦎 🦎🦎🦎🦎🦎🦎 herple.wytamma.com

E. coli be like

They’re not making AGI they’re making money

🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀 Check it out here: doi.org/10.1101/2024... And find the code here: github.com/mbhall88/lrge 🧵👇

Excited to share my first JOSS publication 🎉 Snk: A #Snakemake CLI and Workflow Management System joss.theoj.org/papers/10.21...

I recently released version v1.8 of Beastiary - a tool for real-time and remote monitoring of Bayesian phylogenetic analyses. This version of Beastiary lets you create publicly accessible links to a dashboard of your MCMC github.com/Wytamma/beas... #bioinformatics

Our client side webapp for root-to-tip regression Clockor2 (clockor2.github.io) is now published in Systematic Biology! Check out the paper here -> doi.org/10.1093/sysb... Brainchild of Leo Featherstone in collaboration with @arambaut.bsky.social and Sebastian Duchene