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

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Τίτλος: PangyPlot: multi-scale interactive visualization of pangenome variation graphs.
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.)
References: Bioinformatics. 2015 Oct 15;31(20):3350-2. (PMID: 26099265)
Bioinformatics. 2019 Dec 15;35(24):5318-5320. (PMID: 31368484)
Nature. 2023 May;617(7960):312-324. (PMID: 37165242)
HGG Adv. 2022 Oct 20;4(1):100156. (PMID: 36386424)
Nat Methods. 2024 Nov;21(11):2008-2012. (PMID: 39433878)
Bioinformatics. 2024 Jul 1;40(7):. (PMID: 38960860)
Nat Biotechnol. 2024 Apr;42(4):663-673. (PMID: 37165083)
G3 (Bethesda). 2015 Mar 17;5(5):931-41. (PMID: 25787242)
J Comput Biol. 2018 Jul;25(7):649-663. (PMID: 29461862)
Brief Bioinform. 2018 Jan 1;19(1):118-135. (PMID: 27769991)
Bioinformatics. 2022 Sep 2;38(17):4217-4219. (PMID: 35799353)
Bioinformatics. 2022 Jun 27;38(13):3319-3326. (PMID: 35552372)
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
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  Data: PangyPlot: multi-scale interactive visualization of pangenome variation graphs.
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  Data: <searchLink fieldCode="AU" term="%22Mastromatteo+S%22">Mastromatteo S</searchLink>; 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.<br /><searchLink fieldCode="AU" term="%22Chirmade+S%22">Chirmade S</searchLink>; 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.<br /><searchLink fieldCode="AU" term="%22Roshandel+D%22">Roshandel D</searchLink>; 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.<br /><searchLink fieldCode="AU" term="%22Thiruvahindrapuram+B%22">Thiruvahindrapuram B</searchLink>; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.<br /><searchLink fieldCode="AU" term="%22Wang+Z%22">Wang Z</searchLink>; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.<br /><searchLink fieldCode="AU" term="%22Patel+RV%22">Patel RV</searchLink>; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.<br /><searchLink fieldCode="AU" term="%22Sung+WWL%22">Sung WWL</searchLink>; Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, M5G 1H3, Canada.<br /><searchLink fieldCode="AU" term="%22Hajianpour+A%22">Hajianpour A</searchLink>; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.<br /><searchLink fieldCode="AU" term="%22Wang+C%22">Wang C</searchLink>; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.<br /><searchLink fieldCode="AU" term="%22Lin+F%22">Lin F</searchLink>; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.<br /><searchLink fieldCode="AU" term="%22Keenan+K%22">Keenan K</searchLink>; 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.<br /><searchLink fieldCode="AU" term="%22Avolio+J%22">Avolio J</searchLink>; Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.<br /><searchLink fieldCode="AU" term="%22Eckford+PDW%22">Eckford PDW</searchLink>; Mission Programs, Cystic Fibrosis Canada, Toronto, ON, M4R 1K8, Canada.<br /><searchLink fieldCode="AU" term="%22Ratjen+F%22">Ratjen F</searchLink>; 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.<br /><searchLink fieldCode="AU" term="%22Strug+LJ%22">Strug LJ</searchLink>; 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.
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  Data: 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.<br />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.<br /> (© The Author(s) 2026. Published by Oxford University Press.)
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  Data: Bioinformatics. 2015 Oct 15;31(20):3350-2. (PMID: <searchLink fieldCode="PM" term="%2226099265%22">26099265)</searchLink><br />Bioinformatics. 2019 Dec 15;35(24):5318-5320. (PMID: <searchLink fieldCode="PM" term="%2231368484%22">31368484)</searchLink><br />Nature. 2023 May;617(7960):312-324. (PMID: <searchLink fieldCode="PM" term="%2237165242%22">37165242)</searchLink><br />HGG Adv. 2022 Oct 20;4(1):100156. (PMID: <searchLink fieldCode="PM" term="%2236386424%22">36386424)</searchLink><br />Nat Methods. 2024 Nov;21(11):2008-2012. (PMID: <searchLink fieldCode="PM" term="%2239433878%22">39433878)</searchLink><br />Bioinformatics. 2024 Jul 1;40(7):. (PMID: <searchLink fieldCode="PM" term="%2238960860%22">38960860)</searchLink><br />Nat Biotechnol. 2024 Apr;42(4):663-673. (PMID: <searchLink fieldCode="PM" term="%2237165083%22">37165083)</searchLink><br />G3 (Bethesda). 2015 Mar 17;5(5):931-41. (PMID: <searchLink fieldCode="PM" term="%2225787242%22">25787242)</searchLink><br />J Comput Biol. 2018 Jul;25(7):649-663. (PMID: <searchLink fieldCode="PM" term="%2229461862%22">29461862)</searchLink><br />Brief Bioinform. 2018 Jan 1;19(1):118-135. (PMID: <searchLink fieldCode="PM" term="%2227769991%22">27769991)</searchLink><br />Bioinformatics. 2022 Sep 2;38(17):4217-4219. (PMID: <searchLink fieldCode="PM" term="%2235799353%22">35799353)</searchLink><br />Bioinformatics. 2022 Jun 27;38(13):3319-3326. (PMID: <searchLink fieldCode="PM" term="%2235552372%22">35552372)</searchLink>
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  Data: 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
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