{"doi":"10.1002/cpz1.70236","title":"Setting up JBrowse 2 for Visualizing Genome Synteny","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.","journal":"Current Protocols","year":2025,"id":584294,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.927,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":706666,"name":"Garrett Stevens","orcid":"0000-0002-9781-5323","position":1,"is_corresponding":false},{"id":49665,"name":"Scott Cain","orcid":"0000-0003-0459-9607","position":2,"is_corresponding":false},{"id":14310,"name":"Lincoln Stein","orcid":"0000-0002-1983-4588","position":3,"is_corresponding":false},{"id":382987,"name":"Ian Holmes","orcid":"0000-0001-7639-5369","position":4,"is_corresponding":false},{"id":584246,"name":"Colin Diesh","orcid":"0000-0003-2629-7570","position":0,"is_corresponding":true}],"reference_count":4,"raw_metadata":null,"created_at":"2026-07-19T02:59:11.978098Z","pmid":"41347761","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}