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Felix Wiegand

@fxwiegand.bsky.social
43 followers 13 following 23 posts

👨‍💻 PhD @ Bioinformatics & Computational Oncology, UDE 🧬 Rust, data & science 🎵 Music tech & sonic tinkering 🔗 github.com/fxwiegand

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Felix Wiegand @fxwiegand.bsky.social · 15/09/2026
Our portable alignment viewer #alignoth now supports working with remote BAM files similar to samtools. Simply update to version 1.11 via cargo, conda or pixi and you are good to go. github.com/alignoth/ali... #bioinformatics #genomics #rustlang @johanneskoester.bsky.social
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Felix Wiegand @fxwiegand.bsky.social · 09/09/2026
#datavzrd config files now get autocomplete and inline validation right in your editor thanks to schemastore. Just name the file *.datavzrd.yaml and Zed, VS Code and most other IDEs should pick up the schema automatically. @johanneskoester.bsky.social
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Felix Wiegand @fxwiegand.bsky.social · 07/09/2026
#datavzrd v2.72.2 is out and absolutely worth the update if you build big reports. Generation got a lot faster and memory usage dropped a lot, especially for wide, cross-linked tables. @johanneskoester.bsky.social github.com/datavzrd/dat... #bioinformatics #rustlang #dataviz
github.com
Release v2.72.2 · datavzrd/datavzrd
2.72.2 (2026-09-02) Bug Fixes Render heatmap legends when color-scheme is unset (#1264) (95d04b4) Performance Improvements Cache linked-table column indices across the report (#1263) (b068793) C...
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Felix Wiegand @fxwiegand.bsky.social · 26/08/2026
New in #datavzrd v2.72.0: The suggest command can now draft your report config with any OpenAI compatible LLM endpoint. Describe what you want in plain language and it writes a validated config from your tables. datavzrd.github.io #bioinformatics @johanneskoester.bsky.social
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Robert Aboukhalil @robert.bio · 11/08/2026
I built this because I wanted a way to quickly iterate on the config without re-running the tool each time on the command-line. Feedback is welcome! More anniversary week announcements coming this week: sandbox.bio/anniversary
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Felix Wiegand @fxwiegand.bsky.social · 11/08/2026
@robert.bio created an interactive playground for #datavzrd making it super easy and quick to try out any changes to configuration files and seeing their effect immediately! Very cool! Go and check it out under sandbox.bio/playgrounds/...
sandbox.bio
Interactive datavzrd playground
Playground for creating interactive reports from tabular data using datavzrd
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Robert Aboukhalil @robert.bio · 11/08/2026
Datavzrd is an awesome tool that turns CSVs into shareable reports that can sort/filter/plot your data, made by @fxwiegand.bsky.social and @johanneskoester.bsky.social You can now run Datavzrd in the browser and rebuild the reports in real time as you edit the config: sandbox.bio/playgrounds/...
sandbox.bio
Interactive datavzrd playground
Playground for creating interactive reports from tabular data using datavzrd
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Felix Wiegand @fxwiegand.bsky.social · 10/07/2026
We just released a new version of #alignoth that adds support for multiple bam tracks that will get vstacked. Also many convenience features suggested by @johanneskoester.bsky.social such as automatically creating an index for bam, fasta and vcf files if they dont exit. github.com/alignoth/ali...
github.com
GitHub - alignoth/alignoth: Creating alignment plots from bam files
Creating alignment plots from bam files. Contribute to alignoth/alignoth development by creating an account on GitHub.
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Felix Wiegand @fxwiegand.bsky.social · 26/06/2026
Another new #datavzrd feature has been released in the form of toggling columns into a narrow view. This allows compressing very wide heatmap-heavy tables into an oncoprint like overview. Thanks for the feature suggestion @johanneskoester.bsky.social datavzrd.github.io
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Felix Wiegand @fxwiegand.bsky.social · 12/06/2026
On the fly column reordering is now (or at least once it has reached conda-forge) available in the latest #datavzrd version. I’ll be working on getting this to run in the paginated reports as well so it also becomes available for reports with millions of rows.
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Johannes Köster @johanneskoester.bsky.social · 12/06/2026
#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...
github.com
Release v4.0.0 · rust-bio/rust-bio
4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...
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Felix Wiegand @fxwiegand.bsky.social · 11/06/2026
After some quite time #datavzrd finally got a new release with an updated binning algorithm ensuring interesting datapoints don’t get swallowed up by one bin. Working on more more features right now!
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Universität Duisburg-Essen @unidue.bsky.social · 18/05/2026
Großer Erfolg für die #UDE 🎉: @dfg.de richtet den Sonderforschungsbereich 1752 "DYNAMO" ein. Ab dem 1. Oktober 2026 fördert sie die Forschung zur Verbesserung von Therapien gegen schwarzen #Hautkrebs mit 12,9 Millionen Euro. www.uni-due.de/2026-05-15-n... #SFB
Gruppenbild mit Text: DFG-Förderung. Neuer Sonderforschungsbereich DYNAMO kommt.
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Matthias Flotho @mflot.bsky.social · 16/01/2026
Pretty cool visualization tool for inspecting read alignments! #datavis #bioinformatics #openscience
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Stephen Turner @stephenturner.us · 13/01/2026
Alignoth: portable and interactive visualization of read alignments academic.oup.com/bioinformati... 🧬🖥️🧪 Code (Rust, MIT): github.com/alignoth/ali... Demo: alignoth.github.io/preview.html
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Felix Wiegand @fxwiegand.bsky.social · 08/01/2026
🚀 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
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Jens Zentgraf @rorak.bsky.social · 27/11/2025
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.
doi.org
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co
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Felix Wiegand @fxwiegand.bsky.social · 23/11/2025
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
datavzrd.github.io
Datavzrd: A low-code interactive reporting tool for tabular datasets | Datavzrd v2.61.10 documentation
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Felix Wiegand @fxwiegand.bsky.social · 13/11/2025
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
ALIGNOTH_REPORT | Snakemake wrappers
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Felix Wiegand @fxwiegand.bsky.social · 20/10/2025
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
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Johannes Köster @johanneskoester.bsky.social · 18/09/2025
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.github.io
Vembrane
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Rob Patro @robp.bsky.social · 18/09/2025
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
blog.rust-lang.org
Announcing Rust 1.90.0 | Rust Blog
Empowering everyone to build reliable and efficient software.
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Felix Wiegand @fxwiegand.bsky.social · 05/09/2025
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.
doi.org
Komplexe Tabellen verständlich machen - BIOspektrum
BIOspektrum -
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German Conference on Bioinformatics #GCB2026 @gcb-bioinformatics.bsky.social · 02/09/2025
🧬 & 🖥️ ✨ 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...
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Science X / Phys.org @sciencex.bsky.social · 23/07/2025
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
techxplore.com
New open-source tool makes complex data understandable
Tabular data is at the heart of scientific analysis—whether in medicine, the social sciences, or even archaeology. Making it comprehensible and usable is often a tedious task, especially when the data is extensive or complex.
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Felix Wiegand @fxwiegand.bsky.social · 23/07/2025
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
journals.plos.org
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.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 27/06/2025
Cleanifier: A fast and lightweight k-mer based tool to remove contamination in microbial sequence data www.biorxiv.org/content/10.1101/202…
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Johannes Köster @johanneskoester.bsky.social · 13/06/2025
#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
GitHub - vembrane/vembrane: vembrane filters VCF records using python expressions
vembrane filters VCF records using python expressions - vembrane/vembrane
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Felix Wiegand @fxwiegand.bsky.social · 28/05/2025
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
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Felix Wiegand @fxwiegand.bsky.social · 26/05/2025
@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...
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Johannes Köster @johanneskoester.bsky.social · 15/05/2025
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...
snakemake.readthedocs.io
Changelog | Snakemake 9.4.0 documentation
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Felix Wiegand @fxwiegand.bsky.social · 06/05/2025
🚀 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
github.com
GitHub - alignoth/alignoth: Creating alignment plots from bam files
Creating alignment plots from bam files. Contribute to alignoth/alignoth development by creating an account on GitHub.
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Stephen Turner @stephenturner.us · 14/04/2025
Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data www.biorxiv.org/content/10.1... 🧬🖥️🧪
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Johannes Köster @johanneskoester.bsky.social · 09/04/2025
Our preprint about #datavzrd is finally published: doi.org/10.1101/2025.... Furthermore, #datavzrd has now been downloaded 500k times. datavzrd.github.io
doi.org
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...
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Felix Wiegand @fxwiegand.bsky.social · 08/04/2025
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
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 08/04/2025
Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data www.biorxiv.org/content/10.1101/202…
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Johannes Köster @johanneskoester.bsky.social · 11/02/2025
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...
datavzrd.github.io
Examples | Datavzrd 2.50.0 documentation
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Felix Wiegand @fxwiegand.bsky.social · 29/01/2025
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
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Johannes Köster @johanneskoester.bsky.social · 13/01/2025
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...
github.com
Release v2.46.0 · datavzrd/datavzrd
2.46.0 (2025-01-10) Features Add new subcommand for suggesting configurations based on files (#858) (e460e04) Add publish subcommand (#856) (1c8facc)
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Johannes Köster @johanneskoester.bsky.social · 02/12/2024
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
biorxiv.org
srahunter: a user-friendly tool to speed up and simplify data downloading from NCBI SRA
Easy access and use of vast datasets are paramount for advancing scientific discovery in steadily expanding studies based on high-throughput sequencing (HTS). The Sequence Read Archive (SRA) is a publ...
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Johannes Köster @johanneskoester.bsky.social · 28/11/2024
#datavzrd has a new spell for rendering tables columns containing clinical significance terms (from ClinVar) as colored badges: datavzrd.github.io/docs/spells....
datavzrd.github.io
Spells | Datavzrd 2.43.1 documentation
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