Johannes Köster
Professor for Bioinformatics and Computational Oncology
University of Duisburg-Essen
Author of Snakemake, founder of Bioconda
- I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
- The new #Snakemake releases in the last weeks (9.14.*-9.16) have massively improved the way Snakemake handles source files from github (wrappers, modules, scripts, envs), avoiding the github API entirely and caching (bare) git repos instead. This increases performance and avoid hitting API limits.
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- We have released multiple new #Varlociraptor versions in the last weeks, providing various model improvements that further reduce false positives, improve the performance, and fix bugs with the log2fc operator of Varlcoriaptor's calling grammar. varlociraptor.github.io
- Reposted by Johannes Köster🚀 Our new paper on Alignoth just published in Bioinformatics! Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows. 📄 doi.org/10.1093/bioi... #bioinformatics #genomics #rust @johanneskoester.bsky.social
- #Snakemake 9.14 is released. It integrates with yet another scripting language ( #hy, adding to the already existing #python, #r, #rust, #bash, and #julia support). Further it offers a massively improved local storage footprint. Many thanks to our awesome community! snakemake.github.io
- Reposted by Johannes KösterThe official Datavzrd documentation now includes an AI (trained on docs, code and our paper) to answer all your questions: datavzrd.github.io/docs/index.h... Huge thanks to @gurubase.bsky.social for supporting Open-Source software and making this possible! @johanneskoester.bsky.social
- Reposted by Johannes KösterCheck out our demo hosted on GitHub pages: alignoth.github.io/alignoth-exa... Props to my colleague Felix who worked with me on this over the last few weeks in the @johanneskoester.bsky.social lab.
- Reposted by Johannes KösterWe’ve added a new Snakemake meta-wrapper for creating standalone variant reports: 🔗 snakemake-wrappers.readthedocs.io/en/stable/me... It combines Datavzrd for an interactive overview table with Alignoth for read pileup plots — all linked together in one portable HTML report.
- Reposted by Johannes KösterSuper happy to announce a major update of our portable and interactive alignment viewer #alignoth written in #rust. The new version provides improved highlighting of specific genomic sites or regions via VCF or BED inputs and also updates the coverage plot with variants! @johanneskoester.bsky.social
- The #Snakemake wrapper repository and #Snakedeploy have received a major update: each wrapper now reports the latest version with changes, and #Snakedeploy can automatically upgrade all wrappers in your workflow to those versions. snakemake-wrappers.readthedocs.io
- #Snakemake has a novel feature for generalizing rules and modules: pathvars! snakemake.readthedocs.io/en/stable/sn... Pathvars are particularly useful to make modules parameterizable and more generic. Further, they reduce boilerplate code commonly used for defining output folders.
- Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-... #sciworkflows #reproducibility
- 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
- #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.
- 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...
- Reposted by Johannes KösterHappy 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.
- #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!
- Reposted by Johannes KösterOur 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.
- #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...
- Reposted by Johannes KösterAnother 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
- Reposted by Johannes Köster@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...
- Our preprint about #datavzrd is finally published: doi.org/10.1101/2025.... Furthermore, #datavzrd has now been downloaded 500k times. datavzrd.github.io
- 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.
- 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.
- 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
- 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...
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- 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.
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- An exciting first day of the #SnakemakeHackathon2025 at @cern.bsky.social is ending now. I have already merged several pull requests and many very productive teams have formed!
- Reposted by Johannes KösterThe entire conda "toolchain" is in the process of being rewritten on top of Rust.
- #Snakemake has an update best practices guide: snakemake.readthedocs.io/en/stable/sn...
- #Snakemake 8.29 has been released. It provides various improvements to the integrated reporting, as well as many small bug fixes: snakemake.readthedocs.io/en/stable/pr...
- #rustbio 2.2 has been released. It offers various improvements for FASTA/FASTQ reading and writing. Reverse q-gram/kmer iteration, and improvements for the PSSM implementation. github.com/rust-bio/rus...
- The #Datavzrd docs now show 4 example reports from various disciplines (bioinf, social, astronomy, anthropology). This illustrates how it can replace spreadsheet supplementaries with visual and interactive interfaces. Thanks to @fxwiegand.bsky.social for the work! datavzrd.github.io/docs/example...
- Among these, the #datavzrd version of the supplement of the fascinating Moscot paper from @fabiantheis.bsky.social's lab (doi.org/10.1038/s415...) . datavzrd.github.io/example-repo.... Using the suggest and publish subcommands, such reports are can now be created even faster.
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- Reposted by Johannes Köster🎉 Say hello to py-rattler-build! 📦 Now you can build conda packages directly in Python! It's never been easier. Get started today: rattler.build/latest/refe... Available on conda-forge and PyPI! 🚀
- Reposted by Johannes KösterThe latest #datavzrd version introduces a new pills option to visualize multiple values in a single table cell, with each ordinal value represented by a distinct color. @johanneskoester.bsky.social datavzrd.github.io
- The #snakemake workflow catalog has since recently >300 registered workflows with standardized and unified usage instructions . Furthermore, Michael Jahn from Emmanuelle Charpentier's lab is now the new maintainer of the catalog: snakemake.github.io/snakemake-wo...
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- My PhD student @fxwiegand.bsky.social has released #datavzrd 2.46 (datavzrd.github.io). We have added two new subcommands: "datavzrd suggest" auto-generates a config from given tables. "datavzrd publish" automatically publishes a given report to github pages: github.com/datavzrd/dat...
- The latest two #snakemake releases bring lots of little bug fixes and tow major new features: 1. a helper function for deriving sub-paths of input our output files (e.g. to pass a prefix to a command or script) 2. helpers to dynamically access input/output without writing python functions
- Sorry, there was a mistake in the example rule. Here is the correct one:
- Technically, "output.foo" here returns an ordinary python function which returns the path of the output file named foo when being invoked by Snakemake upon determination of the rule params. The subpath helper function takes a Path, a str, or such a function and returns whatever its args request.
- I have released a new version of #varlociraptor with 3 new features. 1. model now better deals with PCR artifacts on single reads 2. a new HINTS field that gives insight into model decisions 3. multi-bam input for alignment property estimation varlociraptor.github.io
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