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 ;-)

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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
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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

🦠🧬🖥️ 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...

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/...

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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...

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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)