# User guide How to drive JBrowse once it is running. New here? Start with the [JBrowse Web](https://jbrowse.org/jb2/docs/quickstart_web) or [JBrowse Desktop](https://jbrowse.org/jb2/docs/quickstart_desktop) quickstart. ## General usage - [Basic usage](https://jbrowse.org/jb2/docs/user_guides/basic_usage) - [Connections](https://jbrowse.org/jb2/docs/user_guides/connections) - [Editing a track's plot as text](https://jbrowse.org/jb2/docs/user_guides/edit_plot) - [Export R script](https://jbrowse.org/jb2/docs/user_guides/r_export) - [Highlights](https://jbrowse.org/jb2/docs/user_guides/highlights) - [Installing plugins](https://jbrowse.org/jb2/docs/user_guides/plugin_store) - [Opening track hubs by URL](https://jbrowse.org/jb2/docs/user_guides/hub_url) ## Track types - [Alignments track](https://jbrowse.org/jb2/docs/user_guides/alignments_track) - [GC content track](https://jbrowse.org/jb2/docs/user_guides/gc_content_track) - [Gene track](https://jbrowse.org/jb2/docs/user_guides/gene_track) - [GWAS / Manhattan track](https://jbrowse.org/jb2/docs/user_guides/gwas_track) - [Hi-C track](https://jbrowse.org/jb2/docs/user_guides/hic_track) - [MAF track](https://jbrowse.org/jb2/docs/user_guides/maf_track) - [Multi-row feature track](https://jbrowse.org/jb2/docs/user_guides/multirow_feature_track) - [Multi-sample variant display](https://jbrowse.org/jb2/docs/user_guides/multivariant_track) - [Quantitative track](https://jbrowse.org/jb2/docs/user_guides/quantitative_track) - [Sequence track](https://jbrowse.org/jb2/docs/user_guides/sequence_track) - [Variant track](https://jbrowse.org/jb2/docs/user_guides/variant_track) ## Views - [Circular genome view](https://jbrowse.org/jb2/docs/user_guides/circular_view) - [Dotplot view](https://jbrowse.org/jb2/docs/user_guides/dotplot_view) - [Graph genome view](https://jbrowse.org/jb2/docs/user_guides/graph_genome_view) - [Linear synteny view](https://jbrowse.org/jb2/docs/user_guides/linear_synteny_view) - [Spreadsheet view](https://jbrowse.org/jb2/docs/user_guides/spreadsheet_view) - [SV inspector view](https://jbrowse.org/jb2/docs/user_guides/sv_inspector_view) ## Sequence tools - [BLAT and in-silico PCR](https://jbrowse.org/jb2/docs/user_guides/blat) - [Consensus sequence](https://jbrowse.org/jb2/docs/user_guides/consensus_sequence) - [Feature sequence panel](https://jbrowse.org/jb2/docs/user_guides/feature_sequence) - [Sequence search](https://jbrowse.org/jb2/docs/user_guides/sequence_search) ## Analysis - [Clustering rows](https://jbrowse.org/jb2/docs/user_guides/clustering) - [SV visualization](https://jbrowse.org/jb2/docs/user_guides/sv_visualization) ## Tutorials ### genomes.jbrowse.org - [Basic usage of genomes.jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/genomes_basics) - [Synteny on genomes.jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/genomes_synteny) - [Proteins on genomes.jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/genomes_proteins) - [RepeatMasker as one row per class](https://jbrowse.org/jb2/docs/tutorials/repeatmasker_classes) ### Synteny & comparative genomics #### Whole-genome alignments - [Synteny visualization (pairwise minimap2)](https://jbrowse.org/jb2/docs/tutorials/synteny_visualization) - [Comparing one genome's two haplotypes (T2T-HG002)](https://jbrowse.org/jb2/docs/tutorials/hg002_haplotypes) - [Synteny from liftOver chains (hg38 and eight vertebrates)](https://jbrowse.org/jb2/docs/tutorials/hg38_vertebrates_synteny) - [Synteny visualization (all-vs-all minimap2)](https://jbrowse.org/jb2/docs/tutorials/allvsall_synteny) - [Rearrangements between genomes by type (SyRI)](https://jbrowse.org/jb2/docs/tutorials/syri_synteny) - [Synteny on a circle (human and mouse)](https://jbrowse.org/jb2/docs/tutorials/circular_synteny) #### Ortholog tables - [Synteny from MCScan anchors (grape, peach)](https://jbrowse.org/jb2/docs/tutorials/mcscan_synteny_grape_peach) - [Synteny from an ortholog table (grape, peach, cacao)](https://jbrowse.org/jb2/docs/tutorials/multiway_synteny_grape_peach_cacao) - [Synteny visualization (OrthoFinder orthogroups)](https://jbrowse.org/jb2/docs/tutorials/orthofinder_synteny) - [Synteny from gene symbols (eight primates)](https://jbrowse.org/jb2/docs/tutorials/primate_orthologs_synteny) - [Synteny from gene symbols (44 E. coli genomes)](https://jbrowse.org/jb2/docs/tutorials/ecoli_orthologs_synteny) - [Synteny by ancestral linkage group (sponge, comb jelly, jellyfish)](https://jbrowse.org/jb2/docs/tutorials/odp_linkage_groups_synteny) - [Selection pressure between two genomes (dN/dS)](https://jbrowse.org/jb2/docs/tutorials/selection_pressure) - [Synteny visualization (a polyploid against itself)](https://jbrowse.org/jb2/docs/tutorials/homoeolog_synteny) ### Pangenomes - [Pangenome (pggb)](https://jbrowse.org/jb2/docs/tutorials/pangenome_ecoli) - [Pangenome (Minigraph-Cactus)](https://jbrowse.org/jb2/docs/tutorials/pangenome_cactus) - [Pangenome (hosting your own graph)](https://jbrowse.org/jb2/docs/tutorials/pangenome_prepare_graph) - [Pangenome (mouse)](https://jbrowse.org/jb2/docs/tutorials/pangenome_mouse) - [Pangenome (cattle)](https://jbrowse.org/jb2/docs/tutorials/pangenome_cattle) #### HPRC release 2 - [](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc) - [Pangenome (HPRC) part 2: haplotypes against each other](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_haplotypes) - [Pangenome (HPRC) part 3: repeat lengths across haplotypes](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_repeats) ### Structural variation - [CNV across a population (1000 Genomes)](https://jbrowse.org/jb2/docs/tutorials/population_cnv) - [Structural variants (1000 Genomes)](https://jbrowse.org/jb2/docs/tutorials/sv_multisamples) - [Structural variants from Hi-C](https://jbrowse.org/jb2/docs/tutorials/hic_structural_variants) - [Low-mappability regions (SMN)](https://jbrowse.org/jb2/docs/tutorials/mappability_qc) ### Cancer genomics - [Complex rearrangements and derivative alleles](https://jbrowse.org/jb2/docs/tutorials/cancer_sv) - [Gene fusion calls and the DNA behind them](https://jbrowse.org/jb2/docs/tutorials/k562_fusions) - [Reviewing a whole SV callset](https://jbrowse.org/jb2/docs/tutorials/sv_callset_review) - [Structural variants (Cancer GIAB)](https://jbrowse.org/jb2/docs/tutorials/sv_visualization_cgiab) - [Mutation cohort (TCGA)](https://jbrowse.org/jb2/docs/tutorials/tcga_cohort_mutations) - [CNV cohort (TCGA)](https://jbrowse.org/jb2/docs/tutorials/tcga_cohort_cnv) ### Population genomics - [Selection scans (Drosophila DGRP)](https://jbrowse.org/jb2/docs/tutorials/population_genomics) - [Phased trio analysis (1000 Genomes)](https://jbrowse.org/jb2/docs/tutorials/analyze_trio) - [LD at a selective sweep (human)](https://jbrowse.org/jb2/docs/tutorials/ld_human) - [LD across an inversion (mosquitoes)](https://jbrowse.org/jb2/docs/tutorials/ld_mosquitoes) - [QTL mapping (BXD mice)](https://jbrowse.org/jb2/docs/tutorials/bxd_qtl) #### Dog10K - [A selected haplotype (Dog10K)](https://jbrowse.org/jb2/docs/tutorials/dog10k_selection) - [A loss-of-function allele across breeds (Dog10K)](https://jbrowse.org/jb2/docs/tutorials/dog10k_lof) - [Structural variants (Dog10K)](https://jbrowse.org/jb2/docs/tutorials/dog10k_svs) - [Local ancestry (Dog10K)](https://jbrowse.org/jb2/docs/tutorials/local_ancestry) ### Epigenomics & single cell - [Methylation (long-read)](https://jbrowse.org/jb2/docs/tutorials/methylation) - [Methylation (bisulfite)](https://jbrowse.org/jb2/docs/tutorials/bisulfite) - [ChromHMM chromatin states](https://jbrowse.org/jb2/docs/tutorials/chromhmm) - [Single-cell ATAC pseudobulk](https://jbrowse.org/jb2/docs/tutorials/scatac_pseudobulk) - [Single-cell RNA pseudobulk](https://jbrowse.org/jb2/docs/tutorials/scrna_pseudobulk) - [AlphaGenome predictions](https://jbrowse.org/jb2/docs/tutorials/alphagenome) ### Transcriptomics & proteins - [RNA-seq visualization](https://jbrowse.org/jb2/docs/tutorials/rnaseq) - [Differential transcript usage](https://jbrowse.org/jb2/docs/tutorials/dtu) - [TP53 from prediction to crystal](https://jbrowse.org/jb2/docs/tutorials/tp53_structures) ### Genes & annotation - [Reviewing a gene prediction (Tiberius)](https://jbrowse.org/jb2/docs/tutorials/gene_prediction_review) - [Gene density and transposon density along a chromosome](https://jbrowse.org/jb2/docs/tutorials/gene_density) - [A map of the human mitochondrial genome](https://jbrowse.org/jb2/docs/tutorials/organelle_map) ### Grammar of graphics - [A grammar of graphics over a BED (RepeatMasker Alu age)](https://jbrowse.org/jb2/docs/tutorials/alu_age) - [A grammar of graphics over a BAM (NA12878 insert size)](https://jbrowse.org/jb2/docs/tutorials/read_marks) ### Configuration & embedding - [Display settings](https://jbrowse.org/jb2/docs/tutorials/display_settings) - [Embedding JBrowse](https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view) - [JBrowse CLI with Desktop](https://jbrowse.org/jb2/docs/tutorials/cli_desktop) ### Automation - [Driving JBrowse with an AI agent (two Drosophila genomes)](https://jbrowse.org/jb2/docs/tutorials/agent_synteny)