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

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

(2/2)

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!

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
(5/5)

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…
(4/5)

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.
(3/5)

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.
(2/5)

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

(6/6)

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/...

(5/6)

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!

(4/6)

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.

(3/6)

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

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

(2/6)