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

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

Oregon National Primate Research Center

Research output: Contribution to journal › Article › peer-review

34 Scopus citations

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.

Original language	English (US)
Article number	74
Journal	Genome biology
Volume	24
Issue number	1
DOIs	https://doi.org/10.1186/s13059-023-02914-z
State	Published - Dec 2023

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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Diesh, C., Stevens, G. J., Xie, P., De Jesus Martinez, T., Hershberg, E. A., Leung, A., Guo, E., Dider, S., Zhang, J., Bridge, C., Hogue, G., Duncan, A., Morgan, M., Flores, T., Bimber, B. N., Haw, R., Cain, S., Buels, R. M., Stein, L. D., & Holmes, I. H. (2023). JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome biology, 24(1), Article 74. https://doi.org/10.1186/s13059-023-02914-z

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 2023, 'JBrowse 2: a modular genome browser with views of synteny and structural variation', Genome biology, vol. 24, no. 1, 74. https://doi.org/10.1186/s13059-023-02914-z

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

Abstract

ASJC Scopus subject areas

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