Oliver Schwengers
@oschwengers.bsky.social
🦠🧬🖥️ Microbial bioinformatics PostDoc
@JLUGiessen, WGS bacteria, plasmids, software/pipeline developer, father of 2, husband, astrophotographer
@JLUGiessen, WGS bacteria, plasmids, software/pipeline developer, father of 2, husband, astrophotographer
Pinned
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
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...
👇 1/7
@MicrobioSoc
#MGen
>661,000 bacterial genomes, uniformly characterized & annotated, enriched with metadata, accessible via a flexible search engine:
doi.org/10.1099/mgen...
👇 1/7
Reposted by Oliver Schwengers
November 24, 2025 at 9:30 AM
Reposted by Oliver Schwengers
🎉 The de.NBI & ELIXIR-DE All Hands Meeting 2025 kicked off in Berlin!
We celebrated 10 years of de.NBI with a birthday cake 🎂, welcomed new Associated Partners, and connected with 140+ participants. Stay tuned for more! #deNBI2025
We celebrated 10 years of de.NBI with a birthday cake 🎂, welcomed new Associated Partners, and connected with 140+ participants. Stay tuned for more! #deNBI2025
November 20, 2025 at 3:26 PM
🎉 The de.NBI & ELIXIR-DE All Hands Meeting 2025 kicked off in Berlin!
We celebrated 10 years of de.NBI with a birthday cake 🎂, welcomed new Associated Partners, and connected with 140+ participants. Stay tuned for more! #deNBI2025
We celebrated 10 years of de.NBI with a birthday cake 🎂, welcomed new Associated Partners, and connected with 140+ participants. Stay tuned for more! #deNBI2025
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!
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!
October 6, 2025 at 8:11 AM
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!
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 ;-)
(1/2)
To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)
(1/2)
October 6, 2025 at 7:27 AM
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 ;-)
(1/2)
To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)
(1/2)
Reposted by Oliver Schwengers
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...
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
August 8, 2025 at 7:11 AM
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...
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...
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
May 8, 2025 at 1:08 PM
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...
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
(1/5)
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
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
April 28, 2025 at 8:47 AM
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
(1/5)
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
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
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
March 25, 2025 at 9:45 AM
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
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...
👇 1/6
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
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
March 6, 2025 at 8:59 AM
🦠🧬🖥️ 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
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
Reposted by Oliver Schwengers
Our paper on bacterial #Resistance prediction with #Genomics and #MachineLearning reached a milestone with its 120th citation! 🎉 @oschwengers.bsky.social
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Validate User
academic.oup.com
March 5, 2025 at 7:10 PM
Our paper on bacterial #Resistance prediction with #Genomics and #MachineLearning reached a milestone with its 120th citation! 🎉 @oschwengers.bsky.social
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Last week before Christmas...
Though not being a captain, that's the post, ... just that ;-)
Though not being a captain, that's the post, ... just that ;-)
December 18, 2024 at 9:08 AM
Last week before Christmas...
Though not being a captain, that's the post, ... just that ;-)
Though not being a captain, that's the post, ... just that ;-)
Reposted by Oliver Schwengers
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
November 29, 2024 at 11:38 AM
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
Reposted by Oliver Schwengers
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...
github.com/kjolley/BIGS...
PubMLST - Public databases for molecular typing and microbial genome diversity
Public databases for molecular typing and microbial genome diversity
pubmlst.org
November 26, 2024 at 11:23 AM
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...
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
- 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
November 26, 2024 at 8:10 AM
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
- 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/...
👇 (1/11)
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/...
👇 (1/11)
Release v1.10 - Novel in & novel out · oschwengers/bakta
This is the tenth minor release (v1.10) introducing user-provided HMMs, output file recovery, feature inference scores, and various improvements.
Compatible database scheme version: 5
Important
Si...
github.com
November 18, 2024 at 8:49 AM
🦠🧬💻 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/...
👇 (1/11)
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/...
👇 (1/11)
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...
👇 1/7
@MicrobioSoc
#MGen
>661,000 bacterial genomes, uniformly characterized & annotated, enriched with metadata, accessible via a flexible search engine:
doi.org/10.1099/mgen...
👇 1/7
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
November 4, 2024 at 10:33 AM
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...
👇 1/7
@MicrobioSoc
#MGen
>661,000 bacterial genomes, uniformly characterized & annotated, enriched with metadata, accessible via a flexible search engine:
doi.org/10.1099/mgen...
👇 1/7
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...
- bacteria: 30,238 -> 50,226
- archaea: 606 -> 905
- fungi: 347 -> 557
- plasmids: 32,611 -> 81,674
doi.org/10.5281/zeno...
January 12, 2024 at 9:20 AM
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...
- 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)
- 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)
November 29, 2023 at 12:29 PM
🦠🧬💻 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)
- 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)