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☰ Contents
Introduction
Getting started
JBrowse desktop quick start
JBrowse web setup using the CLI
User guide
User guide
Alignments track
Analyze a trio
Basic usage
Bookmark widget
Connections
Dotplot view
Feature sequence panel
Hi-C track
Linear synteny view
Multi-quantitative tracks
Multi-sample variant displays
Plugin store
Quantitative tracks
Sequence track
Structural variant visualization
SV inspector view
Variant tracks
User tutorials
Analyzing a phased trio
Cancer Genome in a Bottle (SVs)
Multi-sample SV visualization w/ 1kG
Synteny visualization and genome alignment
Visualizing DNA methylation
Configuration
Introduction - Config guide
Alignments track configuration
Avoiding stale config
Coloring/theming
Configuring assemblies
Configuring plugins
Configuring tracks
Customizing feature colors with callbacks and plugins
Customizing feature details with callbacks and plugins
Default session
Disabling analytics
FromConfig adapters
Hi-C track configuration
Hierarchical track selector
Intro to the config.json format
Multi-quantitative tracks
Quantitative tracks
Synteny track config
Text searching
Using jexl callbacks
Variant track configuration
Development
Developer guide
Admin server GUI (experimental)
Configuration model basics
Creating custom adapters
Creating custom add-track workflows
Creating custom display types
Creating custom renderers
Creating custom top-level menu items
Creating custom track types
Creating custom view types
Creating custom widgets
Extension points
PIF (Pairwise Indexed Format)
Pluggable elements
RefName aliasing
Renderer architecture
Writing a no-build plugin
Writing a plugin using jbrowse-plugin-template
Embedding JBrowse
Embedded components
JBrowse Jupyter
JBrowseR
Command line tools (JBrowse CLI)
API reference (auto-generated)
Configuration schema
AlignmentsTrack
ArcRenderer
BamAdapter
BaseAssembly
BaseConnection
BaseInternetAccount
BaseLinearDisplay
BaseRpcDriver
BaseTrack
BasicTrack
BedAdapter
BedGraphAdapter
BedGraphTabixAdapter
BedpeAdapter
BedTabixAdapter
BgzipFastaAdapter
BigBedAdapter
BigWigAdapter
BlastTabularAdapter
CanvasFeatureRenderer
ChainAdapter
ChordVariantDisplay
ChromSizesAdapter
CramAdapter
CytobandAdapter
DeltaAdapter
DensityRenderer
DivSequenceRenderer
DotplotDisplay
DotplotRenderer
DropboxOAuthInternetAccount
ExternalTokenInternetAccount
FeatureTrack
FormatAbout
FormatDetails
FromConfigAdapter
FromConfigRegionsAdapter
FromConfigSequenceAdapter
GCContentAdapter
GCContentTrack
Gff3Adapter
Gff3TabixAdapter
GoogleDriveOAuthInternetAccount
GtfAdapter
HicAdapter
HicRenderer
HicTrack
HierarchicalConfigSchema
HtsgetBamAdapter
HTTPBasicInternetAccount
IndexedFastaAdapter
JB2TrackHubConnection
JBrowse1Connection
JBrowse1TextSearchAdapter
JBrowseConfiguration
JBrowseReactCircularGenomeViewConfig
JBrowseReactLinearGenomeViewConfig
JBrowseRootConfig
LDDisplay
LDRenderer
LDTrack
LDTrackDisplay
LGVSyntenyDisplay
LinearAlignmentsDisplay
LinearArcDisplay
LinearBareDisplay
LinearBasicDisplay
LinearComparativeDisplay
LinearFeatureDisplay
LinearGCContentDisplay
LinearGCContentTrackDisplay
LinearGenomeViewConfigSchema
LinearHicDisplay
LinearLollipopDisplay
LinearPairedArcDisplay
LinearPileupDisplay
LinearReadArcsDisplay
LinearReadCloudDisplay
LinearReferenceSequenceDisplay
LinearSNPCoverageDisplay
LinearSyntenyDisplay
LinearVariantDisplay
LinearVariantMatrixDisplay
LinearVariantMatrixRenderer
LinearWiggleDisplay
LinePlotRenderer
MainThreadRpcDriver
MashMapAdapter
MCScanAnchorsAdapter
MCScanSimpleAnchorsAdapter
MultiDensityRenderer
MultiLinearVariantDisplay
MultiLinearWiggleDisplay
MultiLineRenderer
MultiQuantitativeTrack
MultiRowLineRenderer
MultiRowXYPlotRenderer
MultiVariantRenderer
MultiWiggleAdapter
MultiXYPlotRenderer
NcbiSequenceReportAliasAdapter
NCListAdapter
OAuthInternetAccount
PAFAdapter
PairwiseIndexedPAFAdapter
PileupRenderer
PlinkLDAdapter
PlinkLDTabixAdapter
QuantitativeTrack
ReferenceSequenceTrack
RefNameAliasAdapter
RpcOptions
SequenceSearchAdapter
SharedLDDisplay
SharedVariantDisplay
SharedWiggleDisplay
SNPCoverageAdapter
SNPCoverageRenderer
SplitVcfTabixAdapter
StructuralVariantChordRenderer
SvgFeatureRenderer
SyntenyTrack
TrixTextSearchAdapter
TwoBitAdapter
UCSCTrackHubConnection
UnindexedFastaAdapter
VariantTrack
VcfAdapter
VcfTabixAdapter
WebWorkerRpcDriver
WiggleRenderer
XYPlotRenderer
State model
AddTrackModel
AppCoreJBrowseModel
AppFocusMixin
Assembly
AssemblyManager
Base1DView
BaseConnectionModel
BaseDisplay
BaseFeatureWidget
BaseInternetAccountModel
BaseLinearDisplay
BaseRootModel
BaseSessionModel
BaseTrackModel
BaseViewModel
BaseWebSession
BreakpointSplitView
CircularView
ConnectionManagementSessionMixin
DesktopSessionManagementMixin
DesktopSessionModel
DesktopSessionTrackMenuMixin
DialogQueueSessionMixin
DockviewLayoutMixin
Dotplot1DView
DotplotDisplay
DotplotView
DrawerWidgetSessionMixin
FacetedModel
FeatureDensityMixin
GoogleDriveOAuthInternetAccount
GridBookmarkWidgetModel
HierarchicalTrackSelectorWidget
HistoryManagementMixin
InternetAccountsMixin
JB2TrackHubConnection
JBrowseDesktopConfigModel
JBrowseDesktopRootModel
JBrowseDesktopSessionModel
JBrowseReactAppConfigModel
JBrowseReactAppRootModel
JBrowseReactCircularGenomeViewRootModel
JBrowseReactCircularGenomeViewSessionModel
JBrowseReactLinearGenomeViewRootModel
JBrowseReactLinearGenomeViewSessionModel
JBrowseWebConfigModel
JBrowseWebRootModel
JBrowseWebSessionModel
JobsListModel
LDDisplay
LDTrackDisplay
LGVSyntenyDisplay
LinearAlignmentsDisplay
LinearAlignmentsDisplayMixin
LinearArcDisplay
LinearBareDisplay
LinearBasicDisplay
LinearComparativeDisplay
LinearComparativeView
LinearFeatureDisplay
LinearGCContentDisplay
LinearGCContentTrackDisplay
LinearGenomeView
LinearHicDisplay
LinearLollipopDisplay
LinearPairedArcDisplay
LinearPileupDisplay
LinearReadArcsDisplay
LinearReadArcsDisplaySettingsMixin
LinearReadCloudDisplay
LinearReadDisplayBaseMixin
LinearReferenceSequenceDisplay
LinearSNPCoverageDisplay
LinearSyntenyDisplay
LinearSyntenyView
LinearVariantDisplay
LinearVariantMatrixDisplay
LinearWiggleDisplay
MultiLinearVariantDisplay
MultiLinearWiggleDisplay
MultipleViewsSessionMixin
MultiVariantBaseModel
NonBlockCanvasDisplayMixin
ReferenceManagementSessionMixin
RootAppMenuMixin
SessionAssembliesMixin
SessionTracksManagerSessionMixin
SharedGCContentModel
SharedLDModel
SharedLinearPileupDisplayMixin
SharedWiggleMixin
SnackbarModel
SpreadsheetImportWizard
SpreadsheetView
SpreadsheetViewSpreadsheet
SvInspectorView
TemporaryAssembliesMixin
ThemeManagerSessionMixin
TrackHeightMixin
TracksManagerSessionMixin
UCSCTrackHubConnection
WebSessionConnectionsMixin
URL query parameter API
FAQ
Archive
PAG 33 (2026) JBrowse setup and exploration
PAG2023 Workshop
PAG2022 - Synteny visualization using JBrowse Desktop
Analyze a trio