Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/ Best of all, the data never leaves your computer! #phage #phagesky

I'm excited to speak at @keystoneSymposia.bsky.social Beyond #Antibiotics : Emerging Strategies Combating #BacterialInfection, this week! Excited to explore emerging research in Breckenridge! keysym.us/KSBeyondAntibiotics26 #KSBeyondAntibiotics26

Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection | Keystone Symposia

Join us at the Keystone Symposia on Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection, May 2026, in Breckenridge, with field leaders!

keysym.us

Howdy! If you're at #APHL, stop by poster P1012 to learn more about Bactopia and the fun things we're doing at WPHL. Happy to chat about Bactopia v4, my experience with Nextflow v26.04, or just binf in general! P.S. there's stickers and a "poster to go" in postcard form!

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 · 3mo 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

Howdy! Happy to announce that Bactopia v4 is finally out! 🥳 This release supports the latest from @seqera.io Nextflow v26 (strict syntax, static types, and records! oh my!) It also open's the doors to start doing some fun things with Bactopia. To learn more, check out: bactopia.io/blog/bactopi...

Bactopia v4 Updates and Improvements | Bactopia

Learn about the new features and improvements in Bactopia version 4.

bactopia.io

Seems I'm not good at Bactopia v4 progress updates! Since my last update: - Nextflow v25+ compatible - Converted to nf-test - nf-bactopia plugin released If you are interesting in testing (very much appreciated!), I now have a dev build available here: github.com/bactopia/bac...

Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia

Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...

github.com

Mirrors! 🪞 I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly. I started with NCBI taxonomy. What else? lskatz.github.io/mirror/

Another Bactopia update! I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!

Bactopia update! Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon. If you're interested in testing please let me know here or at github.com/bactopia/bac...

skani v0.3.0 is released. github.com/bluenote-157... - 30-40% potential reduction in memory with approximately the same runtime. - Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.

GitHub - bluenote-1577/skani: Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. - bluenote-1577/skani

github.com

Minor Bactopia v4 update, I have a first pass at the Nextflow v25 syntax conversion. I converted a Bactopia Tool to v25, then used @anthropic.com Claude to some help convert the remaining Bactopia Tools. Lots of cleaning still, but progress! See github.com/bactopia/bac... for details on v4!

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...

Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia

Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...

github.com

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight) interpretamr.github.io/AMRrules

Dehosting compressed FASTQ at 150Mbp/s on a MacBook github.com/bede/deacon

At #APHL annual conference? Check out poster 212 to learn more about Bactopia and all the fun things it can do! Side note, this is the first time all of Bactopia is depicted in a single metro map! 🎉 @bactopia.com @nextflow.io @aphl.org Full PDF: datasets.bactopia.com/media/2025-b...

I've made a new framework for developing sequence based typing (SBT) tools. 🐪camlhmp ("camel hump") allows for an SBT schema to be defined in YAML, disentangling the SBT logic from the code, making much easier to maintain. See poster or learn more at: rpetit3.github.io/camlhmp/late...

Thankful for the opportunity to talk at #ASMNGS about the work we're doing at the WPHL 🦬 to further improve Bactopia! (haha also🏔️!) Per the usual, reach out if you have any questions! Slides are available at: bactopia.github.io/latest/impac...

I thought the #ASMNGS #Hackathon was really productive. My team looked for unique markers for F. tularensis in WGS data and we were able to package everything into a github repository that's mostly functional. Thank you @meganphillips.bsky.social and my other teammates! 💻🧫🧬

GitHub - erinyoung/tulatyper: Subtyping of Francisella tularensis subtypes

Subtyping of Francisella tularensis subtypes. Contribute to erinyoung/tulatyper development by creating an account on GitHub.

github.com

👋 Bactopia users! After 5 years of maintaining Bactopia, I need your help! What's next for Bactopia? 🔍 ⁉️ Help shape the next 5 years of Bactopia by filling out this quick survey: forms.gle/2nsFSYJtJ1me... Please repost and share link with colleagues that also use Bactopia! 🎉

Bactopia Usage Survey 2024

Yo! It's me Robert, the developer of Bactopia! Did you know Bactopia has been maintained for over 5 years? Time flies! While I'm very grateful to have support to continue developing Bactopia, after 5...

forms.gle

Bactopia now supports AllTheBacteria assemblies! If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia. To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies bactopia.github.io/latest/blog/...

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2y ago

AllTheBacteria - all bacterial genomes assembled, available and searchable https://www.biorxiv.org/content/10.1101/2024.03.08.584059v1

🎉 Bactopia v3 is here! 🎉 Very excited for this release! Bactopia, the Nextflow pipeline for bacterial genomes, is now faster, packed with more tools, updated docs, and much much more! Many thanks to all the people who helped test and provided feedback! Learn more at: bactopia.github.io/v3.0.0/

Introduction - Bactopia

An extensive workflow to process Nanopore and Illumina sequencing for bacterial genomes.

bactopia.github.io