We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...). You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.

The 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

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.

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

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.

Rust 1.90.0 is out! blog.rust-lang.org/2025/09/18/R... Major features: * lld as the default linker on x86_64-unknown-linux-gnu * cargo workspace publishing support built into cargo * more const context APIs, and stabilization of new useful APIs

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.

🧬 & 🖥️ ✨ Secure your ticket for the German Conference on #Bioinformatics (#GCB2025)! We are excited to welcome you to Düsseldorf starting September 22, 2025. 👉Register now and be part of #GCB2025: gcb2025.de/GCB2025_regi...

A new open-source tool converts tabular data into interactive HTML reports without programming, enabling accessible data visualization and navigation across diverse scientific fields. doi.org/g9t2fn

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

Cleanifier: A fast and lightweight k-mer based tool to remove contamination in microbial sequence data https://www.biorxiv.org/content/10.1101/2025.06.24.661305v1

#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...

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...

🚀 We just released Alignoth v0.14.0! The HTML view now comes with a control panel, read filtering, multi-selection via shift-click, and a more interactive read info table. Check it out: github.com/alignoth/ali... #bioinformatics #rust #genomics #vegalite

Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data www.biorxiv.org/content/10.1... 🧬🖥️🧪

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

Excited to share that our preprint, Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data, is now up on bioRxiv! 🎉 #datavzrd

Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data https://www.biorxiv.org/content/10.1101/2025.04.03.647146v1

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...

The 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

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...

I am thrilled to see #Datavzrd being used to get portable interactive visual output tables in #srahunter: www.biorxiv.org/content/10.1... datavzrd.github.io

#datavzrd has a new spell for rendering tables columns containing clinical significance terms (from ClinVar) as colored badges: datavzrd.github.io/docs/spells....