Academic Journal
PangyPlot: multi-scale interactive visualization of pangenome variation graphs.
| Τίτλος: | PangyPlot: multi-scale interactive visualization of pangenome variation graphs. |
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| Συγγραφείς: | Mastromatteo S; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Chirmade S; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Roshandel D; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Thiruvahindrapuram B; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Wang Z; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Patel RV; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Sung WWL; Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, M5G 1H3, Canada., Hajianpour A; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Wang C; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Lin F; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Keenan K; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.; Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Avolio J; Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada., Eckford PDW; Mission Programs, Cystic Fibrosis Canada, Toronto, ON, M4R 1K8, Canada., Ratjen F; Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.; Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada., Strug LJ; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.; Departments of Statistical Sciences and Computer Science, University of Toronto, Toronto, ON, M5G 1X6, Canada.; Biostatistics Division Dalla Lana School of Public Health, University of Toronto, Toronto, ON, M5S 3E3, Canada. |
| Συλλογικό Έργο: | Canadian Cystic Fibrosis Gene Modifier Consortium |
| Πηγή: | Bioinformatics (Oxford, England) [Bioinformatics] 2026 Aug 03; Vol. 42 (8). |
| Τύπος έκδοσης: | Journal Article; Research Support, Non-U.S. Gov't |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Oxford : Oxford University Press, c1998- |
| Ιατρικοί όροι (MeSH): | Genomics*/methods , Software* , Genome* , Computer Graphics* , Genetic Variation* |
| Περίληψη: | 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. (© The Author(s) 2026. Published by Oxford University Press.) |
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| Grant Information: | 1009794 CF Canada 2022 Basic and Clinical Research Grant; 187014 Cystic Fibrosis Canada and the CIHR Institute of Circulatory and Respiratory Health; 608828 Cystic Fibrosis Canada; Cystic Fibrosis Foundation (STRUG17PO); FRN-167282 Canada CIHR; OGI-148 Government of Canada through Genome Canada and the Ontario Genomics Institute; The Centre for Applied Genomics |
| Contributed Indexing: | Investigator: LJ Strug; K Keenan; F Ratjen; J Rommens; M Solomon; C Bjornson; M Chilvers; A Price; M Parkins; M Derynck; E Brochiero; L Bilodeau; D Mateos-Corral; D Hughes; MJ Smith; N Morrison; J Brusky; A Stephenson; E Tullis; B Quon; J Yehya; WM Leung; A Cantin; L Lands |
| Entry Date(s): | Date Created: 20260819 Date Completed: 20260828 Latest Revision: 20260923 |
| Update Code: | 20260923 |
| PubMed Central ID: | PMC13523859 |
| DOI: | 10.1093/bioinformatics/btag619 |
| PMID: | 42613741 |
| Βάση Δεδομένων: | MEDLINE |
| ISSN: | 1367-4811 |
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| DOI: | 10.1093/bioinformatics/btag619 |