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.

🔬✨ 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...

🦠🧬🖥️ 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/...

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! 🦠💻

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...

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)

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...

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)

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

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)