Oliver Schwengers
@oschwengers.bsky.social
π¦ π§¬π₯οΈ 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 β 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...
π 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...
π 1/7
Reposted by Oliver Schwengers
November 24, 2025 at 9:30 AM
Reposted by Oliver Schwengers
π The de.NBI & ELIXIR-DE All Hands Meeting 2025 kicked off in Berlin!
We celebrated 10 years of de.NBI with a birthday cake π, 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 π, welcomed new Associated Partners, and connected with 140+ participants. Stay tuned for more! #deNBI2025
November 20, 2025 at 3:26 PM
π The de.NBI & ELIXIR-DE All Hands Meeting 2025 kicked off in Berlin!
We celebrated 10 years of de.NBI with a birthday cake π, 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 π, welcomed new Associated Partners, and connected with 140+ participants. Stay tuned for more! #deNBI2025
We would also like to deeply thank @denbi.bsky.social
for the lasting support and funding enabling constant maintenance and development!
for the lasting support and funding enabling constant maintenance and development!
October 6, 2025 at 8:11 AM
We would also like to deeply thank @denbi.bsky.social
for the lasting support and funding enabling constant maintenance and development!
for the lasting support and funding enabling constant maintenance and development!
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!
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)
Please help us to further improve the annotation of bacterial genomes.
Please RT & share
(2/2)
October 6, 2025 at 7:27 AM
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)
Please help us to further improve the annotation of bacterial genomes.
Please RT & share
(2/2)
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)
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!
September 22, 2025 at 11:13 AM
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!
September 22, 2025 at 11:11 AM
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
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 β 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...
100% agreed - exactly that was also our line of thinking.
April 28, 2025 at 9:54 AM
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.
So, please use a proper encryption for sharing - if required.
April 28, 2025 at 9:26 AM
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.
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)
Of course, your data is handled with care automatically discarded after 30 days.
Just give it a try: bakta.computational.bio
(5/5)
Bakta
bakta.computational.bio
April 28, 2025 at 8:47 AM
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)
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, JSONβ¦
(4/5)
Of course, all results are also available for download in various standard file formats: GFF3, GenBank, EMBL, FASTA, TSV, TXT, JSONβ¦
(4/5)
April 28, 2025 at 8:47 AM
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, JSONβ¦
(4/5)
Of course, all results are also available for download in various standard file formats: GFF3, GenBank, EMBL, FASTA, TSV, TXT, JSONβ¦
(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)
By this, Bakta Web dynamically scales out to meet temporal peak demands.
(3/5)
April 28, 2025 at 8:47 AM
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)
By this, Bakta Web dynamically scales out to meet temporal peak demands.
(3/5)
Bakta Web is our web application accompanying Baktaβs 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)
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)
April 28, 2025 at 8:47 AM
Bakta Web is our web application accompanying Baktaβs 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)
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)
We happily present: βBakta Web β rapid and standardized genome annotation on scalable infrastructuresβ @OxUniPress NARβs 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 β 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: βBakta Web β rapid and standardized genome annotation on scalable infrastructuresβ @OxUniPress NARβs 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
Of course, the DB light version was also updated, however DB sizes have barely changed.
(6/6)
(6/6)
March 6, 2025 at 8:59 AM
Of course, the DB light version was also updated, however DB sizes have barely changed.
(6/6)
(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)
github.com/oschwengers/...
(5/6)
Release v1.11 - Database ups and downs Β· 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
March 6, 2025 at 8:59 AM
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)
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 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)
March 6, 2025 at 8:59 AM
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 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)
- 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)
March 6, 2025 at 8:59 AM
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)
- 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)
Numbers of IPS and PSC have grown by 22% and 13%.
(2/6)
March 6, 2025 at 8:59 AM
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)
Numbers of IPS and PSC have grown by 22% and 13%.
(2/6)
π¦ π§¬π₯οΈ 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...
π 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...
π 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
π¦ π§¬π₯οΈ 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...
π 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...
π 1/6
Reposted by Oliver Schwengers
Our paper on bacterial #Resistance prediction with #Genomics and #MachineLearning reached a milestone with its 120th citation! π @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! π @oschwengers.bsky.social
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...