Oliver Schwengers

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...

👇 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

PubMLST - Public databases for molecular typing and microbial genome diversity Public databases for molecular typing and microbial genome diversity

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

Release v1.10.1 · oschwengers/bakta This is the first v1.10 patch release (v1.10.1). Improvements Improved handling of draft genome in circular plots: 0118983 Added N90 to genome statistics: 7abfa9a Fixes Fixed changed Micromamba ...

Community contributions:
Last but not least, I'd like to thank all users & contributors for incredible feedback, ideas and comments.

Just a few hours after v1.10, reports, fixes and contributions helped to patch -> v1.10.1 - absolutely amazing!

github.com/oschwengers/...

Of note:
We updated Bakta using AMRFinderPlus v4.0.3 that introduced a DB change. So, Bakta might crash using existing DBs.

To update/fix this, please, execute the update command Bakta prints to the CLI - or just re-download it:
'bakta_db download'.
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A hard decision, but to streamline further maintenance and allow for novel features, we have to go on…
So, since v1.10 Bakta cannot annotate signal peptides anymore. If you need this feature, please make sure to use Bakta v1.9.4.
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