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Setting up JBrowse 2 for Visualizing Genome Synteny
Colin Diesh1, Garrett Stevens1, Scott Cain2
1Department of Bioengineering, University of California, Berkeley, California.
Abstract:
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.
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