Setting up JBrowse 2 for Visualizing Genome Synteny
JBrowse 2 is an open-source genome browser that provides unique features for visualizing syntenic relationships between multiple genomes. This article describes a protocol for setting up synteny views in JBrowse 2, using an assembly-to-assembly whole-genome alignment example. We detail data preparation steps, including the generation and formatting of whole-genome alignment data into formats compatible with JBrowse 2's synteny visualization capabilities, and show the GUI-driven process for setting up interactive synteny views and generating publication-quality figures. This protocol establishes methods for using JBrowse 2 to explore conserved sequences across multiple genomes. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Using JBrowse 2 to show genomic synteny.
Authors
- Colin Diesh (ORCID: https://orcid.org/0000-0003-2629-7570)
- Garrett Stevens (ORCID: https://orcid.org/0000-0002-9781-5323)
- Scott Cain (ORCID: https://orcid.org/0000-0003-0459-9607)
- Lincoln Stein (ORCID: https://orcid.org/0000-0002-1983-4588)
- Ian Holmes (ORCID: https://orcid.org/0000-0001-7639-5369)
Institutions
- Ontario Institute for Cancer Research (CA)
- University of California, Berkeley (US)
Publication Details
- Journal
- Current Protocols
- Published
- 2025-12-01
- DOI
- https://doi.org/10.1002/cpz1.70236
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Institutes of Health