Whenever I presented Phold, I was frequently asked "can you do the same beyond phages?" We ( @oschwengers.bsky.social @linsalrob.bsky.social @binomicalabs.org et al) finally did it with Baktfold github.com/gbouras13/ba... www.biorxiv.org/content/10.6...

Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky

If you love microbes & Bioinformatics just like us, then we love to see you at to our upcoming @denbi.bsky.social meet-the-experts session @vaam-microbes.bsky.social #VAAM2026 having a chat on Microbial genomics, our tools ( #Bakta, #EDGAR), DBs ( #BakRep, #sORFdb), and much more related & beyond!

de.NBI & ELIXIR Germany@denbi.bsky.social · 5mo ago

📍 Join us at the de.NBI booth at #VAAM! 🦠 Ready to level up your data? Our Meet the Expert sessions start TODAY at 14:00. Stop by for deep dives into: 🧬 Genomics 14:00 🧪 Metaproteomics 15:00 📊 Metagenomics 16:00 Get expert advice and discover our free tools! 👋✨ #Bioinformatics #Microbiology

Very much looking forward to our 10th (anniversary!) Microbial Genomics Training Course provided by #BiGi @denbi.bsky.social in Gießen. 3 days full of free hands-on microbial genomics training - from QC, assembly and annotation to genome submissions and comparative genomics.

de.NBI & ELIXIR Germany@denbi.bsky.social · 5mo ago

🧬 Join the 10th #Microbial #Genomics #Training Course in Gießen! 📅 June 24–26, 2026 | @jlugiessen.bsky.social 🔬 Learn genome assembly, annotation (w/ #Bakta), comparative genomics ( #EDGAR), & more! 💻 Hands-on, custom data consulting, tools 📩 Info: www.denbi.de/training-cou... #Bioinformatics

🔬✨ Tool of the week: #Metagenomic data analysis made easy! 🚀 The Metagenomics-Toolkit offers a complete workflow: from raw Illumina or Nanopore reads 📈 to taxonomic 🦠 and functional 🧬 insights. 📊 Reproducible, publish-ready results. Ready to boost your research? 🌍📝 www.denbi.de/services-acc...

Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org ! Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these. www.ebi.ac.uk/about/news/u...

AlphaFold Database welcomes community datasets

Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

ebi.ac.uk

🦠🧬🖥️ Bakta v1.12.0 is out with tons of tiny improvements and bug fixes, too many to list all: - partial genes on linear seqs - improved errror handlings & runtimes - support Python 3.12 & 3.13 - ... A huge shout out and thank you to all bug reporters and contributors! github.com/oschwengers/...

Release v1.12 - Just do it, but don't crash · oschwengers/bakta

This is the twelfth minor release (v1.12) providing more than 10 minor improvements and many bug fixes improving runtime stability, IO compatibility, and last but not least user experience. Compati...

github.com

Honestly, as a micro binfie, I couldn't feel more honored than to be entrusted with this! 😃 Prokka has served so many so well, and deeply inspired me how to write Bakta. I'm thankful to be part of this open science com, and will do my best to meet these high quality standards. Thanks Torsten! 🦠💻

Torsten Seemann@torstenseemann.bsky.social · 8mo ago

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

We are de.NBI & ELIXIR-DE, came together for our All Hands 2025! #deNBI2025 #ELIXIRDE #AllHands

🎉 The de.NBI & ELIXIR-DE All Hands Meeting 2025 kicked off in Berlin! We celebrated 10 years of de.NBI with a birthday cake 🎂, welcomed new Associated Partners, and connected with 140+ participants. Stay tuned for more! #deNBI2025

Unbelievable, Bakta reached its 1,000th citation! A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features... ...just the entire incredibly supporting binfie community! Without you, Bakta wouldn't be the same. Thank you!

Dear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)

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...

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

biorxiv.org

Our 9th @denbi.bsky.social "Microbial Genomics training course" is now open for registration! 3 sessions full of microbial bioinformatics at JLU Giessen: I: QC & QA, assembly II: regional & functional annotation III: comparative genomics Info & registration: www.denbi.de/training-cou...

We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue doi.org/10.1093/nar/... Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI: bakta.computational.bio (1/5)

Bakta Web – rapid and standardized genome annotation on scalable infrastructures

Abstract. The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensiv

doi.org

Interested in bacterial genomes? Hundreds of thousands, even millions? All annotated, taxonomically classified, integrated with metadata. Easily searchable, viewable, downloadable, in sync with #AllTheBacteria. Then BakRep is for you! Poster P-CM-102 @vaam-microbes.bsky.social #VAAM25

🦠🧬🖥️ New Bakta DB v6.0 released! After a year, it was time for a Bakta database update - and it's a huge one: - IPS: 330.9M - PSC: 135.3M - PSCC: 37M doi.org/10.5281/zeno... 👇 1/6

Our paper on bacterial #Resistance prediction with #Genomics and #MachineLearning reached a milestone with its 120th citation! 🎉 @oschwengers.bsky.social academic.oup.com/bioinformati...

Last week before Christmas... Though not being a captain, that's the post, ... just that ;-)

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

BIGSdb v1.49.1 has been released. This version improves the layout of user registration and admin pages, and provides the option to export LIN code prefixes of specified length in the Export plugin. BIGSdb powers the databases on pubmlst.org and bigsdb.pasteur.fr. github.com/kjolley/BIGS...

PubMLST - Public databases for molecular typing and microbial genome diversity

Public databases for molecular typing and microbial genome diversity

pubmlst.org

Info: We updated our Bakta WEB version: - MUCH faster annotations via optimized Kubernetes nodes and locally-attached databases - Software-Update to v1.10.1 - Database-Update to v5.1 Publicly available at: bakta.computational.bio

🦠🧬💻 Bakta v1.10 - largest update so far: Highlights: - user-provided HMMs: --hmms - output file recovery from JSON files: bakta_io - export of inference metrics: inference.tsv - bypass overlap filters: --skip-filter - improved genome plots github.com/oschwengers/... 👇 (1/11)

Release v1.10 - Novel in & novel out · oschwengers/bakta

This is the tenth minor release (v1.10) introducing user-provided HMMs, output file recovery, feature inference scores, and various improvements. Compatible database scheme version: 5 Important Si...

github.com

Excited to share BakRep - our latest work published in @MicrobioSoc #MGen >661,000 bacterial genomes, uniformly characterized & annotated, enriched with metadata, accessible via a flexible search engine: doi.org/10.1099/mgen... 👇 1/7

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata

Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding...

doi.org

Just released a new ReferenceSeeker DB version with a lovely increase in reference genomes: - bacteria: 30,238 -> 50,226 - archaea: 606 -> 905 - fungi: 347 -> 557 - plasmids: 32,611 -> 81,674 doi.org/10.5281/zeno...

🦠🧬💻 Just released Bakta 1.9.0 with new features & various improvements: - new --regions option to provide pre-annotated feature regions - annotation of spacer & repeat sequences in CRISPR arrays github.com/oschwengers/... More information below 👇 (1/7)