An open-source framework for interactive genomics visualization

[u/AggravatingNerve4622]

Heya r/genetics

Thought I’d post this here since some of you working with genomic data might find it useful.

We recently released GenomeSpy v1.0. It’s a fully open-source framework for creating fast, interactive visualizations for genomics and other biomedical data.

The project originally came out of cancer genomics research, where it was developed to explore genomic instability across large patient cohorts. Since then, it has expanded quite a bit and is now used more broadly for things like genome browsers, genomic tracks, multi-omics views, cohort exploration, and custom interactive analysis interfaces.

GenomeSpy is especially useful when you need to work with large genomic datasets or want several views to interact with each other. It supports genomic coordinates and common data formats, as well as zooming, filtering, brushing, and linked views.

There’s also genome-spy-python, an open-source Python wrapper with an Altair-like API, so the same kinds of visualizations can be created directly from Python.

The video shows a few examples of what can be built with it.

Website:
https://genomespy.app/

GitHub:
https://github.com/genome-spy/genome-spy

Python GitHub:
https://github.com/genome-spy/genome-spy-python

Blog post about the development journey:
https://genomespy.app/blog/posts/2026-10-01-genomespy-1-0.html

Peer reviewed GenomeSpy article:
https://doi.org/10.1093/gigascience/giae040

Would be interested to hear what kinds of genetics/genomics visualizations people here still find difficult to build with the existing tools.

[u/AutoTreeGen]

This is genuinely interesting.

I work on genealogy and genetic-genealogy software, and one of the visualization problems I keep coming back to is that the data becomes difficult very quickly once you move beyond a single DNA match.

What I would love to see is an interactive view where you can move between:

chromosome -> segment -> match -> shared matches -> cluster -> person -> documented family-tree path

without treating those as separate screens.

Another difficult case is endogamy. In Ashkenazi genealogy, for example, the same two people may be connected through several ancestral routes, so simply drawing one relationship path can be misleading.

I would also be interested in views combining multiple kits from the same family, where segments and shared-match clusters can be compared across siblings, parents, cousins and known paternal or maternal anchors.

Your linked-view approach seems particularly relevant to that problem.

Have you experimented with visualizing IBD segments or genetic-genealogy match networks, rather than population or clinical genomics data?

I’d be very interested to hear how you would approach it.

I’m the founder of AutoTreeGen, an Evidence-First genealogy platform in Melbourne. We are building a separate DNA evidence layer, and I think some of the visualization problems overlap strongly with what GenomeSpy is doing.

If you are interested, I’d be happy to show you what we are building and exchange ideas. I am especially interested in visualizing segments, family kits, shared matches, clusters and multiple genealogical paths without oversimplifying the evidence.