Johannes Köster

F1000Research Article: Sustainable data analysis with Snakemake. Read the latest article version by Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Peter C. van Dyken, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Filipe G. Vi...

Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility

GitHub - rust-bio/rust-bio: This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via cont... This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration. - rus...

#rustbio 3.0 is released, providing BEDPE support and an improved API for Myers bitparallel pattern matching. github.com/rust-bio/rus...

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.

Research Laboratory Job: Postdoctoral Research Fellow - Computational Biologist at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA Postdoctoral Research Fellow - Computational Biologist job

Open postdoc position in my former lab at @danafarber.bsky.social and @harvard.edu Medical School (CFCE). A working environment full of nice and smart people! careers.dana-farber.org/job/12169/po...

Komplexe Tabellen verständlich machen - BIOspektrum BIOspektrum -

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.

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)

#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

#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

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!

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.

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

#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

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

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.

GitHub - vembrane/vembrane: vembrane filters VCF records using python expressions vembrane filters VCF records using python expressions - vembrane/vembrane

#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...

Read alignment visualization with alignoth

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

@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...

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...

New release of #rustbio avoiding traceback overhead with partial order alignment (POA) and adding BLOSUM substitiution matrices.

github.com/rust-bio/rus...

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 chall...

Our preprint about #datavzrd is finally published: doi.org/10.1101/2025.... Furthermore, #datavzrd has now been downloaded 500k times. datavzrd.github.io

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

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.

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.

Computational post-doctoral candidate in the field of data science (m/f/d)

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...

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...

Everything should be available now :-)

add: snakemake-interface-logger-plugins by johanneskoester · Pull Request #54742 · bioconda/bioconda-recipes This adds a recipe for the snakemake-interface-logger-plugins package. Please read the guidelines for Bioconda recipes before opening a pull request (PR). General instructions If this PR adds or ...

Thanks for letting me know. The update-PR first requires a new recipes for snakemake-interface-logger-plugins (logging is now possible via plugins as well). I've just created the PR: github.com/bioconda/bio...

This workshop/hackathon was a success on multiple levels. Bringing the particle physics, bioinformatics, and HPC communities together to work was also an excellent knowledge exchange opportunity which gave the HEP community lots of new ideas and plans to improve things across the LHC experiments.

Today, the #SnakemakeHackathon2025 at @cern.bsky.social has ended with the release of Snakemake 9.0! Huge thanks to the amazing participants and all organizers! In total there were 19 new releases within the ecosystem, including hundreds of new features and bug fixes for Snakemake and its plugins!

The third day of the #SnakemakeHackathon2025 at @cern.bsky.social is over. 11 fantastic pull requests have been merged, fixing various bugs, enabling custom logging, improving the docs, and the expressiveness of the language. snakemake.github.io

The second day of the #SnakemakeHackathon2025 is over. Today I have merged 11 fantastic pull requests in the in main snakemake repo alone. And we have our first #Snakemake release during the hackathon, adding integration with xonsh for scripting and helpers for extracting params from input files.

I’m very happy to be supporting this event via our NSF grant on FAIR and Open-Source for high-energy physics. Thanks to the organizers, including DAI’s @matthewfeickert.com
indico.cern.ch/event/1441041/