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User guide

How to drive JBrowse once it is running. New here? Start with the JBrowse Web or JBrowse Desktop quickstart.

General usage

Basic usageNavigation, searching, opening files, and common UI controlsJBrowse 2ConnectionsUCSC track hubs, JB2 track hubs, and JBrowse 1 data directoriesJBrowse 2Editing a track's plot as textAdvanced → Edit plot... in a track's menu shows the track's color, grouping, rows, axis scales and filters as text, the way a config file writes them, with worked examples and a check of what you typeJBrowse 2Export R scriptThe linear genome view's menu writes an R script that redraws the open tracks as an editable ggplot2 figure, reading the same data filesHighlightsMarking genomic regions and returning to themInstalling pluginsThe plugin store, Desktop's global plugins and config.json, and how long each install lastsJBrowse 2Opening track hubs by URLHand someone a link that loads one or more UCSC track hubs with the &hubURL= parameter

Track types

Alignments trackLearn how to show BAM and CRAM filesGC content trackCompute GC content or GC skew directly from a reference sequenceGene trackTranscript display modes, collapsing introns, color by CDS reading frame, coloring transcripts from a file attribute, peptide lettering, and mature peptides on gene/transcript tracksGWAS / Manhattan trackVisualize genome-wide association study results as an interactive Manhattan plotHi-C trackContact matrix displayMAF trackViewing multiple alignment format (MAF) dataMulti-row feature trackPaint one labeled row per sample from a single interval file, with clustering and per-row coloringQuantitative trackBigWig/BedGraph signal tracks, one signal or a whole cohortSequence trackReference sequence displayVariant sample rowsPopulation-level variant viewsVariant trackVCF variant display

Views

Circular genome viewWhole-genome rings of quantitative tracks, with structural variants and synteny drawn as chords and ribbons across the interiorDotplot viewWhole-genome synteny dotplotGraph genome viewDraw a pangenome graph as a graph, from an rGFA, a plain GFA or a gbz-base database, as a track of the linear genome view at any locusLinear synteny viewSide-by-side alignment of two genomesMulti-way synteny displayOne lane per genome under a linear genome viewJBrowse 2Spreadsheet viewImport tabular data as a searchable feature tableSV inspector viewStructural variant spreadsheet and circular view

Sequence tools

BLAT and in-silico PCRMap a sequence to genome coordinates, and find where primers amplifyJBrowse 2Consensus sequenceCall a consensus sequence from aligned reads, and export it as FASTA or VCFFeature sequence panelSequence extraction for selected featuresJBrowse 2Sequence searchSearch the reference sequence for a pattern, CRISPR guide, or named motif list

Analysis

JBrowse 2Clustering rowsReorder a multi-row track's rows by similarity, read the dendrogram, and filter to a subtreeSV visualizationReading structural variant evidence off the reads

Tutorials

genomes.jbrowse.org

Getting started

Synteny & comparative genomics

Whole-genome alignments

Ortholog tables

Pangenomes

Building a graph

HPRC release 2

Mouse and cattle

Structural variation

Cancer genomics

Population genomics

Dog10K

Epigenomics & single cell

Transcriptomics & proteins

Variants on protein structures

Genes & annotation

Grammar of graphics

Configuration & embedding

Automation