Felix Wiegand

Pretty cool visualization tool for inspecting read alignments!
#datavis #bioinformatics #openscience

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

We rely on Vega-Lite for that. This gives us a lot of flexibility like headlessly generating SVGs using the vega-lite-cli tools. It also allows users to embed alignment plots into Datavzrd: alignoth.github.io/alignoth-exa...

🚀 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

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

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

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.

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.

Announcing Rust 1.90.0 | Rust Blog Empowering everyone to build reliable and efficient software.

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

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.

🧬 & 🖥️
✨ 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...

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.

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

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

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

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...

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.

🚀 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... 🧬🖥️🧪

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

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...

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...

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....