Abstract
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. JBrowse 2 retains the core features of the open-source JavaScript genome browser JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. The software readily allows users to share sessions, open multiple genomes or views, and navigate quickly between these views. It can be embedded in a web page, used as a standalone desktop application, or run from Jupyter notebooks or R sessions. Using a plugin framework, developers can create new data adapters, track types, and visualizations. These improvements are enabled by a ground-up redesign of the JBrowse architecture using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
<colin.diesh{at}gmail.com>, <stevens.garrett.j{at}gmail.com>, <peterkxie{at}yahoo.com>, <tere486martinez{at}gmail.com>, <eahershberg{at}gmail.com>, <angelwyan{at}gmail.com>, <emmaguo{at}berkeley.edu>, <shihabdider{at}berkeley.edu>, <Junjun.Zhang{at}oicr.on.ca>, <caroline.bridge{at}oicr.on.ca>, <Gregory.Hogue{at}oicr.on.ca>, <andrew.duncan{at}oicr.on.ca>, <matt.morgan{at}oregonstate.edu>, <floresct{at}oregonstate.edu>, <bimber{at}ohsu.edu>, <Robin.Haw{at}oicr.on.ca>, <scott{at}scottcain.net>, <rbuels{at}gmail.com>, <Lincoln.Stein{at}oicr.on.ca>, <ihh{at}berkeley.edu>