|
1
|
Diesh C, Stevens GJ, Xie P, De Jesus Martinez T, Hershberg EA, Leung A, Guo E, Dider S, Zhang J, Bridge C, Hogue G, Duncan A, Morgan M, Flores T, Bimber BN, Haw R, Cain S, Buels RM, Stein LD, Holmes IH. JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biol 2023; 24:74. [PMID: 37069644 PMCID: PMC10108523 DOI: 10.1186/s13059-023-02914-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Colin Diesh
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | - Garrett J Stevens
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | - Peter Xie
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | | | - Elliot A. Hershberg
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | - Angel Leung
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | - Emma Guo
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | - Shihab Dider
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | - Junjun Zhang
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3 Canada
| | - Caroline Bridge
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3 Canada
| | - Gregory Hogue
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3 Canada
| | - Andrew Duncan
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3 Canada
| | - Matthew Morgan
- Center for Applied Systems and Software, 224 Milne Computer Center, 1800 SW Campus Way, Oregon State University, Corvallis, OR 97331 USA
| | - Tia Flores
- Center for Applied Systems and Software, 224 Milne Computer Center, 1800 SW Campus Way, Oregon State University, Corvallis, OR 97331 USA
| | - Benjamin N. Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006 USA
| | - Robin Haw
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3 Canada
| | - Scott Cain
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3 Canada
| | - Robert M. Buels
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| | - Lincoln D. Stein
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3 Canada
| | - Ian H. Holmes
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720 USA
| |
Collapse
|
|
2
|
De Jesus Martinez T, Hershberg EA, Guo E, Stevens GJ, Diesh C, Xie P, Bridge C, Cain S, Haw R, Buels RM, Stein LD, Holmes IH. JBrowse Jupyter: a Python interface to JBrowse 2. Bioinformatics 2023; 39:btad032. [PMID: 36648320 PMCID: PMC9887080 DOI: 10.1093/bioinformatics/btad032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/10/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
MOTIVATION JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization. RESULTS We have developed a package that provides a Python interface to JBrowse 2's suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google's Colab notebooks, providing reproducible interactive views. AVAILABILITY AND IMPLEMENTATION JBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https://github.com/GMOD/jbrowse-jupyter.
Collapse
Affiliation(s)
| | - Elliot A Hershberg
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA
| | - Emma Guo
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA
| | - Garrett J Stevens
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA
| | - Colin Diesh
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA
| | - Peter Xie
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA
| | - Caroline Bridge
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Scott Cain
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Robin Haw
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Robert M Buels
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA
| | - Lincoln D Stein
- Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Ian H Holmes
- Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
|
3
|
Hershberg EA, Stevens G, Diesh C, Xie P, De Jesus Martinez T, Buels R, Stein L, Holmes I. JBrowseR: An R Interface to the JBrowse 2 Genome Browser. Bioinformatics 2021; 37:3914-3915. [PMID: 34196689 PMCID: PMC8570803 DOI: 10.1093/bioinformatics/btab459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/27/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Genome browsers are an essential tool in genome analysis. Modern genome browsers enable complex and interactive visualization of a wide variety of genomic data modalities. While such browsers are very powerful, they can be challenging to configure and program for bioinformaticians lacking expertise in web development. RESULTS We have developed an R package that provides an interface to the JBrowse 2 genome browser. The package can be used to configure and customize the browser entirely with R code. The browser can be deployed from the R console, or embedded in Shiny applications or R Markdown documents. AVAILABILITY JBrowseR is available for download from CRAN, and the source code is openly available from the Github repository at https://github.com/GMOD/JBrowseR/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Online.
Collapse
Affiliation(s)
- Elliot A Hershberg
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Garrett Stevens
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Colin Diesh
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter Xie
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Robert Buels
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lincoln Stein
- Adaptive Oncology, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Ian Holmes
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA,To whom correspondence should be addressed.
| |
Collapse
|