@lbartels7.bsky.social
Reposted
We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...).
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co
doi.org
November 27, 2025 at 11:27 AM
We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...).
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
Reposted
RE: https://fediscience.org/@snakemake/115611862667755622
Now, this is huge!
Thanks to a contribution from Cade Mirchandani (Santa Cruz, CA), whom I met at this year's #snakemakehackathon users can now supply a partition profile. So, instead of wrangling #Slurm partition information into a […]
Now, this is huge!
Thanks to a contribution from Cade Mirchandani (Santa Cruz, CA), whom I met at this year's #snakemakehackathon users can now supply a partition profile. So, instead of wrangling #Slurm partition information into a […]
Original post on fediscience.org
fediscience.org
November 26, 2025 at 8:21 AM
RE: https://fediscience.org/@snakemake/115611862667755622
Now, this is huge!
Thanks to a contribution from Cade Mirchandani (Santa Cruz, CA), whom I met at this year's #snakemakehackathon users can now supply a partition profile. So, instead of wrangling #Slurm partition information into a […]
Now, this is huge!
Thanks to a contribution from Cade Mirchandani (Santa Cruz, CA), whom I met at this year's #snakemakehackathon users can now supply a partition profile. So, instead of wrangling #Slurm partition information into a […]
Reposted
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 18, 2025 at 9:59 AM
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
Reposted
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Reposted
⚡New Study Uncovers Molecular Drivers of Long #COVID
Researchers from Borstel, Lübeck, and Kiel identify two key messengers that trigger persistent inflammation in the nasal mucosa: fz-borstel.de/en/latest-ne... @uni-kiel.de, #UKSH, #UzL, @leibniz-gemeinschaft.de
Researchers from Borstel, Lübeck, and Kiel identify two key messengers that trigger persistent inflammation in the nasal mucosa: fz-borstel.de/en/latest-ne... @uni-kiel.de, #UKSH, #UzL, @leibniz-gemeinschaft.de
scRNA-seq reveals persistent aberrant differentiation of nasal epithelium driven by TNFα and TGFβ in post-COVID syndrome
Nature Communications - In this work, authors apply single-cell transcriptomics to nasal biopsies from post-COVID syndrome patients, revealing chronic inflammation driven by TNFα and...
rdcu.be
November 8, 2025 at 9:53 AM
⚡New Study Uncovers Molecular Drivers of Long #COVID
Researchers from Borstel, Lübeck, and Kiel identify two key messengers that trigger persistent inflammation in the nasal mucosa: fz-borstel.de/en/latest-ne... @uni-kiel.de, #UKSH, #UzL, @leibniz-gemeinschaft.de
Researchers from Borstel, Lübeck, and Kiel identify two key messengers that trigger persistent inflammation in the nasal mucosa: fz-borstel.de/en/latest-ne... @uni-kiel.de, #UKSH, #UzL, @leibniz-gemeinschaft.de
Reposted
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:19 AM
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted
The Journal "Genome Biology" is calling for submissions to the Collection on the biology of drug resistance and tolerance in #bacteria, #viruses and #fungi. One guest editor is Margo Diricks @fzborstel.bsky.social
www.biomedcentral.com/collections/...
#antibioticresistance #antimicrobialresistance
www.biomedcentral.com/collections/...
#antibioticresistance #antimicrobialresistance
Call for papers - Biology of drug resistance and tolerance in bacteria, viruses, fungi
www.biomedcentral.com
October 31, 2025 at 5:18 PM
The Journal "Genome Biology" is calling for submissions to the Collection on the biology of drug resistance and tolerance in #bacteria, #viruses and #fungi. One guest editor is Margo Diricks @fzborstel.bsky.social
www.biomedcentral.com/collections/...
#antibioticresistance #antimicrobialresistance
www.biomedcentral.com/collections/...
#antibioticresistance #antimicrobialresistance
Reposted
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
github.com
October 21, 2025 at 8:00 PM
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
Reposted
Yesterday’s NGMI3 symposium @fzborstel.bsky.social was a real highlight 🎉 Great keynotes, inspiring discussions & a lot of fun! Many thanks to #NDI3, #Nordinfect & Oliver JT who did such a great job👏
@oneyrolles.bsky.social, @maxgg.bsky.social, Susanne Häussler, Silke Meiners & Christian Karsten!
@oneyrolles.bsky.social, @maxgg.bsky.social, Susanne Häussler, Silke Meiners & Christian Karsten!
October 9, 2025 at 5:09 PM
Yesterday’s NGMI3 symposium @fzborstel.bsky.social was a real highlight 🎉 Great keynotes, inspiring discussions & a lot of fun! Many thanks to #NDI3, #Nordinfect & Oliver JT who did such a great job👏
@oneyrolles.bsky.social, @maxgg.bsky.social, Susanne Häussler, Silke Meiners & Christian Karsten!
@oneyrolles.bsky.social, @maxgg.bsky.social, Susanne Häussler, Silke Meiners & Christian Karsten!
Reposted
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...
www.nature.com/articles/d41...
‘Google for DNA’ brings order to biology’s big data
MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.
www.nature.com
October 9, 2025 at 3:00 PM
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted
What an honor and joy to speak at Borsteler Herrenhaus for #NDI3 2025! Thrilled to reconnect with friends & colleagues. Special thanks to the brilliant students and @carobarisch.bsky.social for the kind invite & flawless organization!
#Immunology #InfectionBiology #NordInfect
Fotos: Kerstin Pukall
#Immunology #InfectionBiology #NordInfect
Fotos: Kerstin Pukall
October 8, 2025 at 6:52 PM
What an honor and joy to speak at Borsteler Herrenhaus for #NDI3 2025! Thrilled to reconnect with friends & colleagues. Special thanks to the brilliant students and @carobarisch.bsky.social for the kind invite & flawless organization!
#Immunology #InfectionBiology #NordInfect
Fotos: Kerstin Pukall
#Immunology #InfectionBiology #NordInfect
Fotos: Kerstin Pukall
Reposted
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!
Reposted
📣 Germany's close to reversing its opposition to mass surveillance & private message scanning, & backing the Chat Control bill. This could end private comms-& Signal-in the EU.
Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.
Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.
We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...
signal.org
October 6, 2025 at 6:46 AM
📣 Germany's close to reversing its opposition to mass surveillance & private message scanning, & backing the Chat Control bill. This could end private comms-& Signal-in the EU.
Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.
Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.
Reposted
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
🦠 Bakterien passen sich schnell an Antibiotika an - aber nicht immer, wie erwartet. Eine neue Studie des @fzb zeigt: Manche Resistenzen machen Haemophilus influenzae gleichzeitig anfälliger für andere Wirkstoffe. Das eröffnet neue Chancen für künftige Therapien journals.asm.org/doi/10.1128/... #AMR
Evolution of beta-lactam resistance causes fitness reductions and several cases of collateral sensitivities in the human pathogen Haemophilus influenzae | Antimicrobial Agents and Chemotherapy
Antimicrobial resistance (AMR) is a major public health challenge globally (1). The World Health Organization has identified several priority pathogens to inform
research and development as well as pu...
journals.asm.org
October 6, 2025 at 7:35 AM
🦠 Bakterien passen sich schnell an Antibiotika an - aber nicht immer, wie erwartet. Eine neue Studie des @fzb zeigt: Manche Resistenzen machen Haemophilus influenzae gleichzeitig anfälliger für andere Wirkstoffe. Das eröffnet neue Chancen für künftige Therapien journals.asm.org/doi/10.1128/... #AMR
Reposted
🦠Bacteria adapt quickly to antibiotics – but not always as expected. A new study from @fzborstel.bsky.social shows: some resistances make Haemophilus influenzae more vulnerable to other drugs. This could open new doors for future therapies:
journals.asm.org/doi/10.1128/... #AMR
journals.asm.org/doi/10.1128/... #AMR
Evolution of beta-lactam resistance causes fitness reductions and several cases of collateral sensitivities in the human pathogen Haemophilus influenzae | Antimicrobial Agents and Chemotherapy
Antimicrobial resistance (AMR) is a major public health challenge globally (1). The World Health Organization has identified several priority pathogens to inform
research and development as well as pu...
journals.asm.org
October 6, 2025 at 7:36 AM
🦠Bacteria adapt quickly to antibiotics – but not always as expected. A new study from @fzborstel.bsky.social shows: some resistances make Haemophilus influenzae more vulnerable to other drugs. This could open new doors for future therapies:
journals.asm.org/doi/10.1128/... #AMR
journals.asm.org/doi/10.1128/... #AMR
Reposted
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
October 2, 2025 at 6:28 AM
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Reposted
💧🦠Wie gelangen #resistente #Bakterien in Teiche, Flüsse & Seen und welche Folgen hat das? Darum geht es in der 6. Folge unseres Podcasts „𝗠𝗶𝗸𝗿𝗼𝗯𝗲𝗻 𝗶𝗺 𝗩𝗶𝘀𝗶𝗲𝗿“.
🎙️Gäste: Alex Greenwood (#IZW) & Hans-Peter Grossart (@igb-berlin.de)
▶️ mikroben-im-visier.podigee.io/6-neue-episode
#Antibiotikaresistenzen
🎙️Gäste: Alex Greenwood (#IZW) & Hans-Peter Grossart (@igb-berlin.de)
▶️ mikroben-im-visier.podigee.io/6-neue-episode
#Antibiotikaresistenzen
September 25, 2025 at 10:16 AM
💧🦠Wie gelangen #resistente #Bakterien in Teiche, Flüsse & Seen und welche Folgen hat das? Darum geht es in der 6. Folge unseres Podcasts „𝗠𝗶𝗸𝗿𝗼𝗯𝗲𝗻 𝗶𝗺 𝗩𝗶𝘀𝗶𝗲𝗿“.
🎙️Gäste: Alex Greenwood (#IZW) & Hans-Peter Grossart (@igb-berlin.de)
▶️ mikroben-im-visier.podigee.io/6-neue-episode
#Antibiotikaresistenzen
🎙️Gäste: Alex Greenwood (#IZW) & Hans-Peter Grossart (@igb-berlin.de)
▶️ mikroben-im-visier.podigee.io/6-neue-episode
#Antibiotikaresistenzen
Reposted
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Phishing site : minimap2.com · Issue #1316 · lh3/minimap2
Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...
github.com
September 9, 2025 at 3:40 PM
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Reposted
📆Save the date. 👉 This year's #BacDive workshop will take place on 24th November 2025, 3 - 5 PM CET online!
Join us for updates and the opportunity to ask questions and provide feedback 🦠🧬.
Write to [email protected] to receive the Zoom login details 🖥️.
Join us for updates and the opportunity to ask questions and provide feedback 🦠🧬.
Write to [email protected] to receive the Zoom login details 🖥️.
September 12, 2025 at 8:34 AM
📆Save the date. 👉 This year's #BacDive workshop will take place on 24th November 2025, 3 - 5 PM CET online!
Join us for updates and the opportunity to ask questions and provide feedback 🦠🧬.
Write to [email protected] to receive the Zoom login details 🖥️.
Join us for updates and the opportunity to ask questions and provide feedback 🦠🧬.
Write to [email protected] to receive the Zoom login details 🖥️.
Reposted
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Reposted
Neue Podcast-Folge mit Elisabeth Pfrommer @rki.de und Christian Nehls @fzborstel.bsky.social. Es geht um resistente Bakterien in der 🐄 🐖 Tierhaltung. Diesmal mit Expertin Tina Kabelitz vom @leibnizatb.bsky.social. #Antibiotikaresistenzen
🎧 Hört rein: mikroben-im-visier.podigee.io/5-neue-episode
🎧 Hört rein: mikroben-im-visier.podigee.io/5-neue-episode
September 4, 2025 at 1:24 PM
Neue Podcast-Folge mit Elisabeth Pfrommer @rki.de und Christian Nehls @fzborstel.bsky.social. Es geht um resistente Bakterien in der 🐄 🐖 Tierhaltung. Diesmal mit Expertin Tina Kabelitz vom @leibnizatb.bsky.social. #Antibiotikaresistenzen
🎧 Hört rein: mikroben-im-visier.podigee.io/5-neue-episode
🎧 Hört rein: mikroben-im-visier.podigee.io/5-neue-episode
Reposted
Check out Ryan's new blogpost, especially if you work on and polish small eukaryotic genome assemblies - it's always nice when someone adds new features for your tools
New blog post!
I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising.
Check it out here:
rrwick.github.io/2025/09/04/h...
I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising.
Check it out here:
rrwick.github.io/2025/09/04/h...
Cross-sample homopolymer polishing with Pypolca
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
September 5, 2025 at 6:20 AM
Check out Ryan's new blogpost, especially if you work on and polish small eukaryotic genome assemblies - it's always nice when someone adds new features for your tools