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!

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

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

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

Genome plots:
To improve Bakta’s circular genome plots, we replaced good old Circos by the novel pure-Python pyCirclize library. Thus, we could also add new features, such as legends and new 'bakta_plot' parameters:
bakta_plot --type cog –dpi 300 --size 8 --label='my custom label text'
(6/11)

As requested from several users, Bakta now writes all annotation metrics (coverage, sequence identities, bitscores, etc) to a dedicated TSV file for further inspection. (4/11)

Recovery of result files:
Bakta’s output too large? Via a new 'bakta_io' cmd all result files can be recovered from its json[.gz] file within seconds.
By this, ~84 Mb of result files (e.g. E.coli) are stored in a 5.8 Mb .json.gz file reducing storage requirements by 93%.
(3/11)

Quick example:
species=="Klebsiella pneumoniae"
+ contig number <= 100
+ completeness >= 0.95
+ contamination <= 0.01
+ containing gene=="mobA"
+ collection-host=="human"
-> 1,545 genomes in <2 sec 😀

5/7