Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!

César de la Fuente@delafuentelab.bsky.social · 2w ago

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

Neue Forschungsgruppe stärkt die funktionelle Mikrobiomforschung am @fzborstel.bsky.social: Prof. Dr. Amelia Barber übernimmt die W3-Professur für „Funktionelle Mikrobiomforschung chronischer Lungenerkrankungen“ und baut am FZB eine neue Forschungsgruppe auf: fz-borstel.de/de/aktuelles...

Finally, I am recruiting a bioinformatic engineer/technician, a lab technician, and a postdoc to help establish the group at @fzborstel.bsky.social (~20km outside Hamburg). More info at: fz-borstel.de/en/education....

Exciting news! After a wonderful four years at @uni-jena.de, I'm excited to announce the next chapter as a group leader at @fzborstel.bsky.social and professor at @uni-kiel.de.

Balance of the Microverse@microverse.bsky.social · last mo.

Congratulations to @ameliabarberphd.bsky.social on her next career step! From July 1, she joins @fzborstel.bsky.social & @uni-kiel.de as Group Leader and Professor. We'll miss her interdisciplinary spirit and fungal expertise. Best of luck in Kiel and Borstel, Amelia! 🦠💻

🧬 PATCH: A toolbox for large-scale pangenomics, from phylogeny to openness prediction. Scales to thousands of genomes! 🛠️ Features: Local alignments, core genome detection, a standardized SOCKS interface, & web tools. 🎓 Free for academics. 👉 www.denbi.de/services-acc... #Bioinformatics #OpenScience

Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)

It is now possible to sponsor #snakemake development. Money will go to the Essen University Medicine Foundation and be used for hackathons, computational resources, and personnel: github.com/sponsors/sna...

Sponsor @snakemake on GitHub Sponsors

Support the development of Snakemake. The money will be used for hackathons, computational resources, and depending on the amount, also personnel.

github.com

Last chance to register for a Scalable genomics course this autumn! It will be a banger. With @katiejenike.bsky.social @richard-durbin.bsky.social @npmalfoy.bsky.social and @vikramshivakumar.bsky.social! coursesandconferences.wellcomeconnectingscience.org/event/scalab...

🏆 Auf der diesjährigen Jahrestagung des Deutsches Zentrum für Lungenforschung hat Tim Hasenbein aus der Forschungsgruppe "Data Science in der Lungenforschung" einen Posterpreis im Bereich "Artificial Intelligence & Digital Tools” gewonnen. 🥳 Herzlichen Glückwunsch zu diesem tollen Erfolg!

🎧 Podcast tip: In the latest episode of "In Conversation With" from the @thelancet.com, Larissa Otero speaks with Prof. Christoph Lange @fzborstel.bsky.social & Prof. Liga Kuksa about their study on long-term outcomes after multidrug-resistant TB treatment in Latvia www.thelancet.com/audio-do/chr...

Christoph Lange and Liga Kuksa on multidrug resistant tuberculosis treatment outcomes

In this episode of In Conversation With, Larissa Otero, senior editor of The Lancet Regional Health Europe, speaks with Professor Christoph Lange (Research Center Borstel, Germany; TB Net) and Profess...

thelancet.com

⚡Save the date! The 48th ‘Northern Germany Meeting on Infection, Immunology & Inflammation (NDI3)’ will take place on 5 November 2026 at @fzborstel.bsky.social. This thrilling event is organised by the Borstel PhDs. Registration opens soon: ndi3.fz-borstel.de

⚡Save the Date! Bereits zum 48. Mal findet am 05. November 2026 das "Northern Germany Meeting on Infection, Immunology & Inflammation (NDI3)" am @fzborstel.bsky.social statt. Organisiert wird diese spannende Veranstaltung von den Borsteler PhDs. Die Anmeldung startet bald: ndi3.fz-borstel.de

Another #Snakemake release (9.22.0). We have added a new default pathvar, new semantic helpers for choosing directories or files from alternatives, extended provenance information and Python 3.14 support. In addition various bugs have been fixed. snakemake.github.io

1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blaster

@denbi.bsky.social will support the #Lipidomics Forum 2026 with a LIFS Training Workshop 📅 Monday, Sept 7, 2026 | 10:00 - 16:30 📍 11th Lipidomics Forum, Borstel (On-Site) 🌱 Fee: 20 € Master tools like LipidXplorer, Skyline, & LipidCompass 🔗 For more information see: www.denbi.de/training-cou...

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

Our paper on efficient capped-depth downsampling is out in GigaByte! 🚀 We added a new "sweep-line" algorithm to rasusa (v3.0.0) that enforces a strict depth cap at every position, while keeping the random selection rasusa is known for. 🧵 1/4 📚 doi.org/10.46471/gig... 💻 github.com/mbhall88/ras...

Efficient downsampling of genome alignments with Rasusa

Efficient downsampling of genome alignments with Rasusa

doi.org

Neue #Podcast Folge: 🧬 Wie Pilze krank machen 💊 Wieso Resistenzen zunehmen 🌍 Welche Rolle Umwelt & Klima spielen 🎧 „Mikroben im Visier“ mit Prof. Dr. Bernhard Hube @leibniz-hki.de @leibniz-gemeinschaft.de mikroben-im-visier.podigee.io/13-neue-epis... #Infektionen #Mikrobiologie #Antimykotika

🚨 CALL FOR APPLICATIONS CLOSES TODAY 🚨 Today is the LAST DAY to submit your abstracts for the ISCB Student Council Symposium 2026! 📍 Location: Washington, DC 📅 Event Date: July 12, 2026 ⏰ Submission Deadline: April 9 👉 Submit through the link in bio! #SCS2026 #ISCB #Bioinformatics

Visit the @denbi.bsky.social posters today at the @vaam-microbes.bsky.social poster sessions

🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See github.com/snakemake/sn... for more

GitHub - snakemake/snakefmt: The uncompromising Snakemake code formatter

The uncompromising Snakemake code formatter. Contribute to snakemake/snakefmt development by creating an account on GitHub.

github.com

You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium): taxonium.org/atb That's a big tree! (unless you're used to SC2 trees)

I just discovered #snakesee from Nils Homer: github.com/nh13/snakesee. This is a nice approach to monitor all running snakemake workflows.

GitHub - nh13/snakesee: A terminal UI for monitoring Snakemake workflows

A terminal UI for monitoring Snakemake workflows. Contribute to nh13/snakesee development by creating an account on GitHub.

github.com

Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....

GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.

A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt

github.com

Really cool paper from Laura Dabos, Inssaf Nedjari & Alejandro Couce at @cbgpmadrid.bsky.social Cryptic phenotypic variation emerges rapidly during the adaptive evolution of a carbapenemase doi.org/10.1038/s415...

Cryptic phenotypic variation emerges rapidly during the adaptive evolution of a carbapenemase - Nature Ecology & Evolution

Experimental characterization of the pathways by which the carbapenemase KPC-2 evolves high activity against ceftazidime reveals strong epistasis underpinning four major resistance groups, each with d...

doi.org

🧬 5th BioHackathon Germany – Save the Date! 📍 Göttingen | 📅 Dec 7–11, 2026 Mark your calendars! We’re bringing together life scientists, bioinformaticians, and data stewards for an intense week of hacking. 💻✨ 🚀 Mid-April: Project applications open 🔗 www.denbi.de/de-nbi-event... #BioHackathon

Very much looking forward to our 10th (anniversary!) Microbial Genomics Training Course provided by #BiGi @denbi.bsky.social in Gießen. 3 days full of free hands-on microbial genomics training - from QC, assembly and annotation to genome submissions and comparative genomics.

de.NBI & ELIXIR Germany@denbi.bsky.social · 5mo ago

🧬 Join the 10th #Microbial #Genomics #Training Course in Gießen! 📅 June 24–26, 2026 | @jlugiessen.bsky.social 🔬 Learn genome assembly, annotation (w/ #Bakta), comparative genomics ( #EDGAR), & more! 💻 Hands-on, custom data consulting, tools 📩 Info: www.denbi.de/training-cou... #Bioinformatics

Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! I'll keep maintaining it. github.com/shenwei356/s...

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit

Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

github.com

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...