JBrowse 2

Overview

JBrowse 2 is a next-generation, open-source genome browser designed for interactive visualization and analysis of genomic data. It supports a wide variety of data types, including BAM, CRAM, VCF, GFF, BED, BigBed, and BigWig, enabling researchers to explore and interpret complex datasets. JBrowse 2 features tightly-integrated linear, circular, dotplot, and synteny views for improved visualization of structural variants and genome synteny. It also offers in-browser protein 3D structure displays with integrated alignment and phylogenetic tree views. The browser is highly extensible via a plugin ecosystem, allowing users to add custom view types, track types, data adapters, and more. It can run on the web, on a desktop, or embedded in an application. JBrowse 2 aims to be a pluggable, open-source computational platform integrating many kinds of biological data.

Common tasks

Visualize genomic data from various file formats (BAM, CRAM, VCF, GFF, BED, BigWig).Display genome annotations and features.Compare genome structures using dotplots and synteny views.Integrate and display protein 3D structures with genomic variants.Customize the browser with plugins to add new features and data types.Browse genomes locally on a desktop.Embed JBrowse 2 within other applications.