PangyPlot: multi-scale interactive visualization of pangenome variation graphs.

Scott Mastromatteo; Shalvi Chirmade; Delnaz Roshandel; Bhooma Thiruvahindrapuram; Zhuozhi Wang; Rohan V Patel; Wilson W L Sung; Amirhossein Hajianpour; Cheng Wang; Fan Lin; Katherine Keenan; Julie Avolio; Paul D W Eckford; Felix Ratjen; Canadian Cystic Fibrosis Gene Modifier Consortium; Lisa J Strug

doi:10.1093/bioinformatics/btag619

PubMed · 42613741

PangyPlot: multi-scale interactive visualization of pangenome variation graphs.

Scott Mastromatteo·Shalvi Chirmade·Delnaz Roshandel·Bhooma Thiruvahindrapuram·Zhuozhi Wang·Rohan V Patel·Wilson W L Sung·Amirhossein Hajianpour·Cheng Wang·Fan Lin·Katherine Keenan·Julie Avolio·Paul D W Eckford·Felix Ratjen·Canadian Cystic Fibrosis Gene Modifier Consortium·Lisa J Strug

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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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Software Genomics Genome Computer Graphics Genetic Variation Journal Article Research Support, Non-U.S. Gov't

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Scott Mastromatteo, Shalvi Chirmade, Delnaz Roshandel, Bhooma Thiruvahindrapuram, Zhuozhi Wang, Rohan V Patel, Wilson W L Sung, Amirhossein Hajianpour, Cheng Wang, Fan Lin, Katherine Keenan, Julie Avolio, Paul D W Eckford, Felix Ratjen, Canadian Cystic Fibrosis Gene Modifier Consortium, Lisa J Strug. 2026-08-03. PangyPlot: multi-scale interactive visualization of pangenome variation graphs.. https://doi.org/10.1093/bioinformatics%2Fbtag619

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