VRPG: an interactive visualization framework for reference-projected pangenome graph
Abstract With the increasing availability of high-quality genome assemblies, pangenome graph is emerging as a new paradigm in the genomics field for identifying, encoding, and interpreting genomic variation landscape at both population and species levels. However, it remains a major challenge in understanding and interpretating pangenome graph via biologically informative visualization. To facilitate a better examination of pangenome graph towards novel biological insights, here we present VRPG, a web-based interactive visualization framework of pangenome graph. VRPG provides dynamic and efficient supports for exploring and annotating pangenome graphs along a reference-based coordinate system. Moreover, VRPG shines with its unique features in highlighting the directed path of any graph-constitutive assembly as well as in denoting copy number variation of genomic segments represented by graph-constitutive nodes, which are highly valuable in genome comparison and variant analysis. Additionally, VRPG enables side-by-side visualization between pangenome graph and reference-based annotation features, bridging the graph and linear genome context. To further demonstrate its features and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of high-quality genome assemblies via a dedicated website (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://www.evomicslab.org/app/vrpg/">https://www.evomicslab.org/app/vrpg/</jats:ext-link>).Contact:<jats:email>yuejiaxinggmail.com</jats:email>Key points Developed an intuitive visualization framework for pangenome graph.Empowered graph-based feature highlighting and variant visualization.Enabled connecting reference-based annotation features in the context of pangenome graph..
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Preprint| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
bioRxiv.org - (2024) vom: 16. Apr. Zur Gesamtaufnahme - year:2024 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Miao, Zepu [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| doi: |
10.1101/2023.01.20.524991 |
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| PPN (Katalog-ID): |
XBI038471701 |
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| 520 | |a Abstract With the increasing availability of high-quality genome assemblies, pangenome graph is emerging as a new paradigm in the genomics field for identifying, encoding, and interpreting genomic variation landscape at both population and species levels. However, it remains a major challenge in understanding and interpretating pangenome graph via biologically informative visualization. To facilitate a better examination of pangenome graph towards novel biological insights, here we present VRPG, a web-based interactive visualization framework of pangenome graph. VRPG provides dynamic and efficient supports for exploring and annotating pangenome graphs along a reference-based coordinate system. Moreover, VRPG shines with its unique features in highlighting the directed path of any graph-constitutive assembly as well as in denoting copy number variation of genomic segments represented by graph-constitutive nodes, which are highly valuable in genome comparison and variant analysis. Additionally, VRPG enables side-by-side visualization between pangenome graph and reference-based annotation features, bridging the graph and linear genome context. To further demonstrate its features and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of high-quality genome assemblies via a dedicated website (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://www.evomicslab.org/app/vrpg/">https://www.evomicslab.org/app/vrpg/</jats:ext-link>).Contact:<jats:email>yuejiaxinggmail.com</jats:email>Key points Developed an intuitive visualization framework for pangenome graph.Empowered graph-based feature highlighting and variant visualization.Enabled connecting reference-based annotation features in the context of pangenome graph. | ||
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