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Oliver Schwengers

@oschwengers.bsky.social

630 followers 71 following 49 posts

🦠🧬🖥️ Microbial bioinformatics PostDoc @JLUGiessen, WGS bacteria, plasmids, software/pipeline developer, father of 2, husband, astrophotographer

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Oliver Schwengers @oschwengers.bsky.social · Nov 4

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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BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata

Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding...

doi.org

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Oliver Schwengers @oschwengers.bsky.social · 4d

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

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Oliver Schwengers @oschwengers.bsky.social · 4d

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!

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Oliver Schwengers @oschwengers.bsky.social · 4d

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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Oliver Schwengers @oschwengers.bsky.social · 4d

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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Oliver Schwengers @oschwengers.bsky.social · 18d

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!

Oliver Schwengers @oschwengers.bsky.social · 18d

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

Reposted by Oliver Schwengers

George Bouras @gbouras13.bsky.social · Aug 8

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...

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...

www.biorxiv.org

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Oliver Schwengers @oschwengers.bsky.social · May 8

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...

9th Microbial Genomics training course

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformati...

www.denbi.de

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Oliver Schwengers @oschwengers.bsky.social · Apr 28

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

Oliver Schwengers @oschwengers.bsky.social · Apr 28

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.

Oliver Schwengers @oschwengers.bsky.social · Apr 28

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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Bakta

bakta.computational.bio

Oliver Schwengers @oschwengers.bsky.social · Apr 28

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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Oliver Schwengers @oschwengers.bsky.social · Apr 28

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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Oliver Schwengers @oschwengers.bsky.social · Apr 28

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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Oliver Schwengers @oschwengers.bsky.social · Apr 28

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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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

doi.org

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Oliver Schwengers @oschwengers.bsky.social · Mar 25

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

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Oliver Schwengers @oschwengers.bsky.social · Mar 6

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

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Oliver Schwengers @oschwengers.bsky.social · Mar 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/...

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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...

github.com

Oliver Schwengers @oschwengers.bsky.social · Mar 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!

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Oliver Schwengers @oschwengers.bsky.social · Mar 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.

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Oliver Schwengers @oschwengers.bsky.social · Mar 6

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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Oliver Schwengers @oschwengers.bsky.social · Mar 6

🦠🧬🖥️ 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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Bakta database

This data repository contains the mandatory DB for Bakta. It is available in two versions: the default (db.tar.gz or) and a lightweight alternative (db-light.tar.gz). Bakta is a tool for the rapid & s...

doi.org

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Reposted by Oliver Schwengers

Heiderlab @heiderlab.bsky.social · Mar 5

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

academic.oup.com/bioinformati...

Validate User

academic.oup.com

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Oliver Schwengers @oschwengers.bsky.social · Dec 18

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

Reposted by Oliver Schwengers

Martin Hunt @martibartfast.bsky.social · Nov 29

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

TNA documentation — TNA 0.0.1 documentation

tna.readthedocs.io

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