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JBrowse 2
The next-generation genome browser·jbrowse.org
JBrowse 2 is a genome browser that can run in a web browser, as a desktop application, or embedded within another app. It provides multiple simultaneous view types (linear, circular, dotplot, synteny, breakpoint split, SV inspector, tabular) for visualizing structural variants, genome synteny, and other genomic data. It supports common bioinformatics formats such as BAM, CRAM, VCF, GFF, BED, BigBed, and BigWig, and features an extensible plugin ecosystem for adding new view types, track types, and data adapters.
What it's for
Browsing genomic data along a reference sequenceVisualizing structural variants and chromosomal translocationsComparing whole genome alignments or synteny datasetsViewing protein 3D structure alongside alignment and phylogenetic tree dataEmbedding genome browser views into other web applicationsAnalyzing Hi-C contact matricesFiltering and sorting BAM/CRAM alignments by tagOpening tabular genomic data formats like BED, VCF, CSV, TSV
Features 18
- Breakpoint split view for long split alignments or paired-end reads across chromosomes
- Circular view showing chromosomal translocations and VCF breakend features as arcs
- Dotplot view for zoomable comparison of whole genome alignments or synteny datasets
- Embeddable as React / NPM components
- Hi-C contact matrix support
- In-app plugin store
- In-browser protein 3D structure display integrated with alignment and phylogenetic tree views
- Large database of pre-loaded species
- Linear genome view with multiple tracks, zooming, navigation, and split view
- Linear synteny view for exploring syntenic alignments
- Plugin ecosystem to add view types, track types, and data adapters
- Sort, color, and filter alignments by BAM/CRAM tag
- Support for BAM, CRAM, tabix-indexed VCF, GFF, BED, BigBed, BigWig and specialized formats
- SV inspector with spreadsheet-like view of structural variants linked to a circular overview
- SVG export of the current view
- Tabular view for opening BED, VCF, CSV, TSV, or bespoke formats like STAR-fusion output
- UCSC track hub support
- Web worker and WASM speed optimizations
At a glance
free tieropen sourceself-hostableAPI
TypeWeb app
DeploymentHybrid
PlatformsWeb
CompanyEvolutionary Software Foundation, Inc.
Integrations
ShinyJupyter
Resources