PangyPlot - a pangenome reference browser

Mastromatteo et al. Beyond reference bias: Making pangenomes accessible with PangyPlot. bioRxiv. 2025.10.31.684064. https://doi.org/10.1101/2025.10.31.684064

PangyPlot (ˈpæŋ-ɡi-plɑt) is a genome graph visualization tool designed to offer intuitive and interactive visualization of genomic data. It enables researchers and biologists to effectively visualize and analyze complex genomic structures and variations.

For "pan-curious" users interested in public data

Preloaded with HPRC v.1.1: https://pangyplot.research.sickkids.ca/

SCREENSHOT WILL GO HERE

For "pan-genious" experts with their own data

Prerequisites

• Graph in GFA format
• Python 3.11 or higher recommended
• Python packages: flask, flask-babel, numpy, bitarray, matplotlib, pympler, python-dotenv
• odgi required to prepare custom data.

Usage - Quick Start

git clone https://github.com/ScottMastro/pangyplot.git
cd pangyplot
python pangyplot.py run --db hprc.clip --ref GRCh38 --annotations gencode48.chrY

This should launch a local web server at http://127.0.0.1:5700 with chrY data that is included with the codebase. Please consult this documentation page for further usage information and test datasets: https://pangyplot.readthedocs.io/en/latest/advanced/quickstart.html

Documentation

License

Acknowledgements

PangyPlot is powered by

---

The tool is provided as-is and may be updated or withdrawn without notice. This tool is intended for research and educational purposes only. Outputs are not intended for clinical, diagnostic, or therapeutic use.