JBrowse 2: a modular genome browser with views of synteny and structural variation

Colin Diesh; Garrett J Stevens; Peter Xie; Teresa De Jesus Martinez; Elliot A. Hershberg; Angel Leung; Emma Guo; Shihab Dider; Junjun Zhang; Caroline Bridge; Gregory Hogue; Andrew Duncan; Matthew Morgan; Tia Flores; Benjamin N. Bimber; Robin Haw; Scott Cain; Robert M. Buels; Lincoln D. Stein; Ian H. Holmes

doi:10.1186/s13059-023-02914-z

Genome Biology (Apr 2023)

JBrowse 2: a modular genome browser with views of synteny and structural variation

Colin Diesh,
Garrett J Stevens,
Peter Xie,
Teresa De Jesus Martinez,
Elliot A. Hershberg,
Angel Leung,
Emma Guo,
Shihab Dider,
Junjun Zhang,
Caroline Bridge,
Gregory Hogue,
Andrew Duncan,
Matthew Morgan,
Tia Flores,
Benjamin N. Bimber,
Robin Haw,
Scott Cain,
Robert M. Buels,
Lincoln D. Stein,
Ian H. Holmes

Affiliations

Colin Diesh: Department of Bioengineering, Stanley Hall, University of California
Garrett J Stevens: Department of Bioengineering, Stanley Hall, University of California
Peter Xie: Department of Bioengineering, Stanley Hall, University of California
Teresa De Jesus Martinez: Department of Bioengineering, Stanley Hall, University of California
Elliot A. Hershberg: Department of Bioengineering, Stanley Hall, University of California
Angel Leung: Department of Bioengineering, Stanley Hall, University of California
Emma Guo: Department of Bioengineering, Stanley Hall, University of California
Shihab Dider: Department of Bioengineering, Stanley Hall, University of California
Junjun Zhang: Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre
Caroline Bridge: Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre
Gregory Hogue: Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre
Andrew Duncan: Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre
Matthew Morgan: Center for Applied Systems and Software, 224 Milne Computer Center, 1800 SW Campus Way, Oregon State University
Tia Flores: Center for Applied Systems and Software, 224 Milne Computer Center, 1800 SW Campus Way, Oregon State University
Benjamin N. Bimber: Oregon National Primate Research Center, Oregon Health and Science University
Robin Haw: Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre
Scott Cain: Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre
Robert M. Buels: Department of Bioengineering, Stanley Hall, University of California
Lincoln D. Stein: Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre
Ian H. Holmes: Department of Bioengineering, Stanley Hall, University of California

DOI: https://doi.org/10.1186/s13059-023-02914-z
Journal volume & issue: Vol. 24, no. 1
pp. 1 – 21

Abstract

Read online

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.

Published in Genome Biology

ISSN: 1474-760X (Online)
Publisher: BMC
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General): Genetics
Website: https://genomebiology.biomedcentral.com/

About the journal