Johannes Köster
@johanneskoester.bsky.social
890 followers 31 following 57 posts
Professor for Bioinformatics and Computational Oncology University of Duisburg-Essen Author of Snakemake, founder of Bioconda
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johanneskoester.bsky.social
Our tool #vembrane has a new homepage, providing a high level summary of all the things you can do with it to transform VCF/BCF files via simple Python expressions: vembrane.github.io
Filter, tag, annotate, sort, and flexibly convert to CSV/TSV, JSON, JSONL, YAML and FHIR via a unified syntax.
Vembrane
vembrane.github.io
Reposted by Johannes Köster
fxwiegand.bsky.social
Happy to share our invited article “Komplexe Tabellen verständlich machen” just published in BIOspektrum: doi.org/10.1007/s122... about our tool #datavzrd @johanneskoester.bsky.social

⚠️ Disclaimer: The article is in German.
Komplexe Tabellen verständlich machen - BIOspektrum
BIOspektrum -
doi.org
johanneskoester.bsky.social
#Varlociraptor 8.7.4 is released. It provides a major performance improvement, leading to potentially dramatically decreased computational complexity for certain event definitions containing fold changes. github.com/varlocirapto...
#variant_calling #genomics
Release v8.7.4 · varlociraptor/varlociraptor
8.7.4 (2025-09-02) Bug Fixes improved CLI help messages (fb9a608) Performance Improvements restrict formula evaluation recursion by allowed values according to log2fc operands (#513) (3dc3074)
github.com
johanneskoester.bsky.social
#Snakemake 9.10 has been released. The major change is that it now supports scheduling plugins. By that your scheduling algorithm research becomes immediately usable with thousands of workflows by thousands of users. snakemake.github.io
Snakemake
snakemake.github.io
johanneskoester.bsky.social
Next year in march, the 2nd #Snakemake hackathon, this time at the #TUMunich in Germany, will take place. If you are interested in participating, follow the link on snakemake.github.io and check out the details!
Snakemake
snakemake.github.io
Reposted by Johannes Köster
fxwiegand.bsky.social
Our paper on Datavzrd has been published in @plosone.org! 🥳
Datavzrd is a new tool written in Rust for creating interactive, shareable HTML reports from tabular data — no server needed.
Check it out here:
🔗 journals.plos.org/plosone/arti...

@johanneskoester.bsky.social
Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data
Tabular data, often scattered across multiple tables, is the primary output of data analyses in virtually all scientific fields. Exchange and communication of tabular data is therefore a central challenge. We present Datavzrd, a tool for creating portable, visually rich, interactive reports from tabular data in any kind of scientific discipline. Datavzrd unifies the strengths of currently common generic approaches for interactive visualization like R Shiny with the portability, ease of use and sustainability of plain spreadsheets. The generated reports do not require the maintenance of a web server nor the installation of specialized software for viewing and can simply be attached to emails, shared via cloud services, or serve as manuscript supplements. They can be specified without requiring imperative programming, thereby enabling rapid development and offering accessibility for non-computational scientists, unlocking the look and feel of dedicated manually crafted web applications without the maintenance and development burden. Datavzrd reports scale from small tables to thousands or millions of rows and offer the ability to link multiple related tables, allowing to jump between corresponding rows or hierarchically explore growing levels of detail.
journals.plos.org
johanneskoester.bsky.social
#vembrane, our CLI tool for manipulating VCF/BCF files via Python expressions has gained a new subcommand for sorting. Use it to sort by impact, pathogenicity, frequencies, or any complex Python logic, e.g. for variant prioritization.
github.com/vembrane/vem...
#genomics #bioinformatics
github.com
johanneskoester.bsky.social
There have been 7 new #Snakemake releases since my last post in May. The most important new feature is --omit-flags, which allows you to deactivate individual input/output flags like "pipe" for the entire workflow (e.g. for debugging). Apart from that, many bugs have been fixed.

snakemake.github.io
Snakemake
snakemake.github.io
johanneskoester.bsky.social
Tip of the day: I have extended the auto-rendered docs of all snakemake executor plugins to give more information on how to best use them. Example: snakemake.github.io/snakemake-pl..., see the usage section.
Snakemake executor plugin: slurm | Snakemake plugin catalog
snakemake.github.io
johanneskoester.bsky.social
#vembrane, our tool for filtering and transforming VCF files with easy to read Python expressions has just gained a new subcommand for directly generating #HL7 #FHIR observations from VCF records. Thanks to Till Hartmann for the continued maintenance!
github.com/vembrane/vem...
GitHub - vembrane/vembrane: vembrane filters VCF records using python expressions
vembrane filters VCF records using python expressions - vembrane/vembrane
github.com
Reposted by Johannes Köster
fxwiegand.bsky.social
Another major new #alignoth release is now available on #bioconda ⭐ Our read alignment plots now include a coverage plot on top as well as improved visualization of overlapping read pairs! Check out our interactive demo at alignoth.github.io/preview.html

@johanneskoester.bsky.social
Read alignment visualization with alignoth
Reposted by Johannes Köster
fxwiegand.bsky.social
@johanneskoester.bsky.social and I just released alignoth v0.15.0! 🎉 Now with a brand-new interactive mode: just run alignoth and follow the prompts—no CLI arguments needed.

github.com/alignoth/ali...
johanneskoester.bsky.social
Whoops, there have been 19 new #Snakemake releases since my last update. Apart from a lot of little bug fixes, we had several usability improvements for resource and temp handling and support for more checksum algorithms when validating output files. snakemake.readthedocs.io/en/stable/pr...
Changelog | Snakemake 9.4.0 documentation
snakemake.readthedocs.io
johanneskoester.bsky.social
New release of #rustbio avoiding traceback overhead with partial order alignment (POA) and adding BLOSUM substitiution matrices.

github.com/rust-bio/rus...
johanneskoester.bsky.social
And finally, here the quick link to the docs. The chatbot can be accessed with the green "Ask AI" button at the bottom right:
snakemake.readthedocs.io
johanneskoester.bsky.social
As always with LLM's, be careful with the answers though. Although they seem quite good in my first tests, I am sure there can be situations where the bot is wrong. In the best case, you take the answers as a starting point and read our original sections in the source docs linked out at the bottom.
johanneskoester.bsky.social
This feels pretty huge! The #Snakemake docs now have an LLM powered chatbot (provided for free by @gurubase.bsky.social). It can be seen as a replacement for the normal doc search. This can help a lot, in particular when you are unsure about the keywords to use for a doc search.
johanneskoester.bsky.social
Open postdoc position in an extremely exciting collaboration project between Becker lab at Max Planck Institute for Molecular Physiology Dortmund and my lab: www.mpi-dortmund.mpg.de/aktuelles/jo...
Computational post-doctoral candidate in the field of data science (m/f/d)
www.mpi-dortmund.mpg.de
johanneskoester.bsky.social
There have been several new #Snakemake releases in the last days. Apart from various fixes, the most important new feature is the ability to annotate input file access patterns. This enables storage backends tailor their provisioning mechanism for each file: snakemake.readthedocs.io/en/stable/sn...
Snakemake
snakemake.github.io
johanneskoester.bsky.social
Everything should be available now :-)