Oliver Schwengers

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...

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

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...

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...

🦠🧬🖥️ 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

We would also like to deeply thank @denbi.bsky.social
for the lasting support and funding enabling constant maintenance and development!

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!

Isolates or MAGs, we're looking for the worst-annotated genomes, i.e. high fraction of CDS w/o any functional annotation. Any public/shareable bacterial genome is highly welcome!

Please help us to further improve the annotation of bacterial genomes.

Please RT & share

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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 ;-)

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Definitely the best to put next. We'll soon start some internal discussion of how/when to integrate that. It's been a pleasure to meet you in person Zam!

Thanks so much Migle! It's been a pleasure to meet you at IMMEM and I'm glad you find BakRep useful!

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...

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...

100% agreed - exactly that was also our line of thinking.

Thanks @kblin.bsky.social for pointing out. Of course, it is not a proper encryption, however hard to guess.

So, please use a proper encryption for sharing - if required.

Even without registration, results can easily and safely be shared with others using encrypted URLs.

Of course, your data is handled with care automatically discarded after 30 days.

Just give it a try: bakta.computational.bio
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Results are presented via a cross-referenced data table, a linear genome browser and circular genome plots - just choose your viz!

Of course, all results are also available for download in various standard file formats: GFF3, GenBank, EMBL, FASTA, TSV, TXT, JSON…
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All executions are conducted in a scalable Kubernetes backend hosted within the @denbiOffice cloud.

By this, Bakta Web dynamically scales out to meet temporal peak demands.
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Bakta Web is our web application accompanying Bakta’s CLI version.

It provides interactive widgets supporting users with both, the provision of input data and sample/sequence metadata, and the interpretation of annotation results.
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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

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
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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

Of course, the DB light version was also updated, however DB sizes have barely changed.

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Release v1.11 - Database ups and downs · oschwengers/bakta This is the eleventh minor release (v1.11) introducing database schema version 6. Compatible database scheme version: 6 Important From this release on, Bakta will use xz instead of gz for all data...

This introduced a DB major scheme update from v5 to v6, which in turned resulted in a new software release v1.11.0:

github.com/oschwengers/...

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Due to this massive increase in known protein sequences, DB size has grown from 72GB to 83GB (deflated).

To mitigate negative download effects for our users, we therefore switched tarball compressions from gzip to xz.

Thus, compressed DB size actually decreased from 37GB to 30GB!

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To further improve annotation quality, external annotation sources have also been updated:

- COG: 2020 -> 2024
- Pfam: 36 -> 37.2
- RefSeq: r220 -> r228
- Rfam: 14.10 -> 15
- UniProtKB: 2023_05 -> 2025_01

Also, NCBI AMRFinderPlus and VFDB have been updated to the most recent versions.

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This is a massive increase in known protein sequences - which is great!

Numbers of IPS and PSC have grown by 22% and 13%.

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🦠🧬🖥️ 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...

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

academic.oup.com/bioinformati...