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.