📄 New paper out in Bioinformatics!
We introduce Alignoth: a lightweight CLI tool for generating portable, self-contained, interactive HTML visualizations of read alignments — no server, no GUI, works headless on clusters & workflows.
✨ Interactive pileups
📦 Single-file HTML (shareable & privacy-friendly)
🦀 Implemented in Rust
👉 https://doi.org/10.1093/bioinformatics/btaf663
The official Datavzrd documentation now includes an AI (trained on docs, code and our paper) to answer all your questions: https://datavzrd.github.io/docs/index.html
Huge thanks to @gurubaseio for supporting Open-Source software and making this possible! @johanneskoester
We’ve added a new Snakemake meta-wrapper for creating standalone variant reports:
🔗 https://snakemake-wrappers.readthedocs.io/en/stable/meta-wrappers/bio/alignoth_report.html
It combines Datavzrd for an interactive overview table with Alignoth for read pileup plots — all linked together in one portable HTML report.
Check out our demo hosted on GitHub pages: https://alignoth.github.io/alignoth-example-report/variants/index_1.html
Props to my colleague Felix who worked with me on this over the last few weeks in the @johanneskoester lab.
#snakemake #bioinformatics #genomics
Happy to share our invited article “Komplexe Tabellen verständlich machen” just published in BIOspektrum: https://doi.org/10.1007/s12268-025-2553-2 about our tool #datavzrd @johanneskoester
⚠️ Disclaimer: The article is in German.
@rupdecat
Thanks for the mention. Yes, this is exactly what #datavzrd is made for. Write an easy #yaml definition of how you want your columns rendered, and datavzrd gives you an interactive, self-contained HTML table.
And @fxwiegand wrote a great #OpenAcess article, that showcases all of its capabilities very nicely. It's a quick (and very visual) read, so I highly recommend having a quick look:
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0323079
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.
@digiresacademy tagging @johanneskoester for https://datavzrd.github.io/ as an alternative, here.
Edit: ah, should have tagged @fxwiegand and @dlaehnemann, too. 😊
Anyhow, I expect the tool to have its impact. It is relatively new, though.
@yokofakun
It's never too late to use the #yaml format. Maybe some useful links can help?
https://koesterlab.github.io/data-science-for-bioinfo/data_formats/yaml.html
Otherwise, I think the datavzrd help and examples are almost self-explanatory, so you can just start from them and replicate the structure whichever way needed...
Great Work, @fxwiegand! Both the tool, and the paper!
And to anyone interested: The paper is a quick read and has really great figures, showcasing how easy it is to get from a TSV (or parquet, or...) file to an interactive HTML table, that you can explore in the browser. You only need a YAML file that defines how to treat your columns, and you can even autogenerate that for a given table input.
Our paper on Datavzrd has been published in @PLOS 🥳
Datavzrd is a new tool written in Rust for creating interactive, shareable HTML reports from tabular data — no server needed. Check it out here:
🔗 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0323079
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.
dlaehnemann
Christian Meesters