Johannes Köster
@johanneskoester.bsky.social
Professor for Bioinformatics and Computational Oncology
University of Duisburg-Essen
Author of Snakemake, founder of Bioconda
University of Duisburg-Essen
Author of Snakemake, founder of Bioconda
Reposted by Johannes Köster
Check 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.
Props to my colleague Felix who worked with me on this over the last few weeks in the @johanneskoester.bsky.social lab.
alignoth.github.io
November 13, 2025 at 10:30 AM
Check 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.
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 Köster
We’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.
🔗 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.
ALIGNOTH_REPORT | Snakemake wrappers
snakemake-wrappers.readthedocs.io
November 13, 2025 at 10:29 AM
We’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.
🔗 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 Köster
Super 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
October 20, 2025 at 11:15 AM
Super 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
The Snakemake Wrappers repository | Snakemake wrappers
snakemake-wrappers.readthedocs.io
October 19, 2025 at 9:15 PM
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.
Pathvars are particularly useful to make modules parameterizable and more generic. Further, they reduce boilerplate code commonly used for defining output folders.
Snakefiles and Rules | Snakemake 9.13.3 documentation
snakemake.readthedocs.io
October 19, 2025 at 9:12 PM
#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.
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
#sciworkflows #reproducibility
Snakemake Hackathon March 2026
We are excited to announce the Snakemake Hackathon 2026, to be held 9-13 March, 2026 at the Technical University Munich. This event will bring together passionate developers and data scientists to col...
indico.cern.ch
October 17, 2025 at 4:49 PM
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
#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
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
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...
f1000research.com
September 23, 2025 at 10:18 AM
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
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...
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...
github.com
September 19, 2025 at 1:01 PM
#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.
Filter, tag, annotate, sort, and flexibly convert to CSV/TSV, JSON, JSONL, YAML and FHIR via a unified syntax.
Vembrane
vembrane.github.io
September 18, 2025 at 6:53 PM
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.
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...
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
careers.dana-farber.org
September 15, 2025 at 10:57 AM
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 Köster
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.
⚠️ Disclaimer: The article is in German.
Komplexe Tabellen verständlich machen - BIOspektrum
BIOspektrum -
doi.org
September 5, 2025 at 7:07 AM
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.
⚠️ 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
#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
September 3, 2025 at 10:11 AM
#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
#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
Snakemake
snakemake.github.io
August 29, 2025 at 12:54 PM
#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!
Snakemake
snakemake.github.io
August 29, 2025 at 10:46 AM
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 Köster
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 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
July 23, 2025 at 7:54 AM
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 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
github.com/vembrane/vem...
#genomics #bioinformatics
github.com
July 21, 2025 at 10:05 AM
#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/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
snakemake.github.io
Snakemake
snakemake.github.io
July 7, 2025 at 3:23 PM
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.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.
Snakemake executor plugin: slurm | Snakemake plugin catalog
snakemake.github.io
June 18, 2025 at 5:19 PM
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...
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
June 13, 2025 at 9:44 AM
#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.com/vembrane/vem...
Reposted by Johannes Köster
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
May 28, 2025 at 10:56 AM
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
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...
github.com/alignoth/ali...
May 26, 2025 at 12:23 PM
@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...
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...
Changelog | Snakemake 9.4.0 documentation
snakemake.readthedocs.io
May 15, 2025 at 2:03 PM
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...
github.com/rust-bio/rus...
May 14, 2025 at 9:51 AM
New release of #rustbio avoiding traceback overhead with partial order alignment (POA) and adding BLOSUM substitiution matrices.
github.com/rust-bio/rus...
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
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...
doi.org
April 9, 2025 at 11:50 AM
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.
April 7, 2025 at 1:36 PM
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.