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JBrowse 2: a modular genome browser with views of synteny and structural variation
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. I...
| Autores principales: | , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
BioMed Central
2023
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108523/ https://www.ncbi.nlm.nih.gov/pubmed/37069644 http://dx.doi.org/10.1186/s13059-023-02914-z |
| _version_ | 1785026866283806720 |
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| author | Diesh, Colin Stevens, Garrett J Xie, Peter De Jesus Martinez, Teresa Hershberg, Elliot A. Leung, Angel Guo, Emma Dider, Shihab Zhang, Junjun Bridge, Caroline Hogue, Gregory Duncan, Andrew Morgan, Matthew Flores, Tia Bimber, Benjamin N. Haw, Robin Cain, Scott Buels, Robert M. Stein, Lincoln D. Holmes, Ian H. |
| author_facet | Diesh, Colin Stevens, Garrett J Xie, Peter De Jesus Martinez, Teresa Hershberg, Elliot A. Leung, Angel Guo, Emma Dider, Shihab Zhang, Junjun Bridge, Caroline Hogue, Gregory Duncan, Andrew Morgan, Matthew Flores, Tia Bimber, Benjamin N. Haw, Robin Cain, Scott Buels, Robert M. Stein, Lincoln D. Holmes, Ian H. |
| author_sort | Diesh, Colin |
| collection | PubMed |
| description | We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02914-z. |
| format | Online Article Text |
| id | pubmed-10108523 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2023 |
| publisher | BioMed Central |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-101085232023-04-18 JBrowse 2: a modular genome browser with views of synteny and structural variation Diesh, Colin Stevens, Garrett J Xie, Peter De Jesus Martinez, Teresa Hershberg, Elliot A. Leung, Angel Guo, Emma Dider, Shihab Zhang, Junjun Bridge, Caroline Hogue, Gregory Duncan, Andrew Morgan, Matthew Flores, Tia Bimber, Benjamin N. Haw, Robin Cain, Scott Buels, Robert M. Stein, Lincoln D. Holmes, Ian H. Genome Biol Software We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02914-z. BioMed Central 2023-04-17 /pmc/articles/PMC10108523/ /pubmed/37069644 http://dx.doi.org/10.1186/s13059-023-02914-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
| spellingShingle | Software Diesh, Colin Stevens, Garrett J Xie, Peter De Jesus Martinez, Teresa Hershberg, Elliot A. Leung, Angel Guo, Emma Dider, Shihab Zhang, Junjun Bridge, Caroline Hogue, Gregory Duncan, Andrew Morgan, Matthew Flores, Tia Bimber, Benjamin N. Haw, Robin Cain, Scott Buels, Robert M. Stein, Lincoln D. Holmes, Ian H. JBrowse 2: a modular genome browser with views of synteny and structural variation |
| title | JBrowse 2: a modular genome browser with views of synteny and structural variation |
| title_full | JBrowse 2: a modular genome browser with views of synteny and structural variation |
| title_fullStr | JBrowse 2: a modular genome browser with views of synteny and structural variation |
| title_full_unstemmed | JBrowse 2: a modular genome browser with views of synteny and structural variation |
| title_short | JBrowse 2: a modular genome browser with views of synteny and structural variation |
| title_sort | jbrowse 2: a modular genome browser with views of synteny and structural variation |
| topic | Software |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108523/ https://www.ncbi.nlm.nih.gov/pubmed/37069644 http://dx.doi.org/10.1186/s13059-023-02914-z |
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