# User guide

How to drive JBrowse once it is running. New here? Start with the
[JBrowse Web](https://jbrowse.org/jb2-staging/docs/quickstart_web) or
[JBrowse Desktop](https://jbrowse.org/jb2-staging/docs/quickstart_desktop) quickstart.

## General usage

- [](https://jbrowse.org/jb2-staging/docs/user_guides/basic_usage)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/bookmark_widget)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/connections)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/display_defaults)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/hub_url)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/plugin_store)

## Track types

- [](https://jbrowse.org/jb2-staging/docs/user_guides/alignments_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/gc_content_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/gene_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/gwas_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/hic_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/maf_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/multiquantitative_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/multirow_feature_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/multivariant_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/multiway_synteny_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/quantitative_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/sequence_track)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/variant_track)

## Views

- [](https://jbrowse.org/jb2-staging/docs/user_guides/circular_view)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/dotplot_view)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/graph_genome_view)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/linear_synteny_view)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/spreadsheet_view)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/sv_inspector_view)

## Sequence tools

- [](https://jbrowse.org/jb2-staging/docs/user_guides/blat)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/consensus_sequence)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/feature_sequence)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/sequence_search)

## Analysis

- [](https://jbrowse.org/jb2-staging/docs/user_guides/clustering)
- [](https://jbrowse.org/jb2-staging/docs/user_guides/sv_visualization)

## Tutorials

### genomes.jbrowse.org

- [](https://jbrowse.org/jb2-staging/docs/tutorials/genomes_basics)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/genomes_synteny)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/genomes_proteins)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/repeatmasker_classes)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/genomes_pangenome)

### Synteny & comparative genomics

- [](https://jbrowse.org/jb2-staging/docs/tutorials/synteny_visualization)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/allvsall_synteny)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/hg002_haplotypes)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/pangenome_ecoli)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/pangenome_cactus)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/pangenome_hprc)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/selection_pressure)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/multiway_synteny_grape_peach_cacao)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/mcscan_synteny_grape_peach)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/homoeolog_synteny)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/orthofinder_synteny)

### Structural variation

- [](https://jbrowse.org/jb2-staging/docs/tutorials/sv_multisamples)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/population_cnv)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/mappability_qc)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/dog10k_svs)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/hic_structural_variants)

### Cancer genomics

- [](https://jbrowse.org/jb2-staging/docs/tutorials/sv_visualization_cgiab)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/tcga_cohort_cnv)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/cancer_sv)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/k562_fusions)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/tcga_cohort_mutations)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/sv_callset_review)

### Population genomics

- [](https://jbrowse.org/jb2-staging/docs/tutorials/population_genomics)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/analyze_trio)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/ld_human)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/ld_mosquitoes)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/bxd_qtl)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/dog10k_lof)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/dog10k_selection)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/local_ancestry)

### Epigenomics & single cell

- [](https://jbrowse.org/jb2-staging/docs/tutorials/methylation)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/bisulfite)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/chromhmm)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/scatac_pseudobulk)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/alphagenome)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/scrna_pseudobulk)

### Transcriptomics & proteins

- [](https://jbrowse.org/jb2-staging/docs/tutorials/rnaseq)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/dtu)

### Configuration & embedding

- [](https://jbrowse.org/jb2-staging/docs/tutorials/display_settings)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/embed_linear_genome_view)
- [](https://jbrowse.org/jb2-staging/docs/tutorials/cli_desktop)