PangyPlot: multi-scale interactive visualization of pangenome variation graphs

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ID: 325565
2026
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Abstract
SUMMARY: Pangenome variation graphs integrate multiple samples into a unified representation, mitigating the reference bias inherent to linear genomes. However, these graphs can be large and structurally complex. Existing visualization tools are each confined to a fixed scale of resolution, requiring researchers to switch between multiple tools to examine variation at different levels of detail. PangyPlot is an interactive pangenome browser designed for multi-scale exploration of reference variation graphs from full chromosome to nucleotide-level sequence segments. PangyPlot anchors navigation to linear reference coordinates, organizes variation into hierarchical bubble structures, and uses a force-directed layout engine for automatic node arrangement. AVAILABILITY AND IMPLEMENTATION: An instance preloaded with data is available at https://pangyplot.research.sickkids.ca. Source code and documentation are openly available at https://github.com/strug-hub/pangyplot under the MIT License.
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Authors Scott Mastromatteo, Shalvi Chirmade, Delnaz Roshandel, Bhooma Thiruvahindrapuram, Zhuozhi Wang, Rohan Patel, Wilson W L Sung, Amirhossein Hajianpour, Cheng Wang, Fan Lin, Katherine Keenan, Julie Avolio, Paul Eckford, Felix Ratjen, Lisa J Strug, Katherine Keenan, Felix Ratjen, Johanna Rommens, M Solomon, Candice Bjornson, Mark Chilvers, April Price, M Parkins, Michael Derynck, Emmanuelle Brochiero, Lara Bilodeau, Dimas Mateos‐Corral, Daniel Hughes, M. Smith, Nancy Morrison, Janna Brusky, A Stephenson, Elizabeth Tullis, Bradey Quon, Jaled Yehya, Winnie M. Leung, Andre Cantin, Larry Lands, Lisa J Strug
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag619
URL
https://doi.org/10.1093/bioinformatics/btag619
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