JBrowse: a dynamic web platform for genome visualization and analysis.

Robert Buels,Monica Munoz-Torres,Ian H Holmes,David M Goodstein,Lincoln Stein,Eric Yao,Gregg Helt,Colin M Diesh,Suzanna E Lewis,Christine G Elsik,Richard D Hayes

doi:10.1186/s13059-016-0924-1

Abstract

BackgroundJBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page.ResultsOverall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication.ConclusionsJBrowse is a mature web application suitable for genome visualization and analysis.

Highlights

JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5
Buels et al Genome Biology (2016) 17:66 platform; releases are tested on Mozilla-based browsers (e.g., Firefox), WebKit browsers (e.g., Safari, Chrome) and Microsoft Internet Explorer, and on desktop and mobile platforms
General improvements to speed and scalability since the last published report include threefold on-disk compression on the server, optimizations to scripts for processing large files, filesystem-oriented optimizations allowing for highly fragmented data, and compression of JSON data

Summary

Introduction

JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is embedded into websites or apps but can be served as a standalone web page. The rest of this paper reviews various operational aspects of JBrowse, starting with the user interface (UI) and user experience and proceeding to describe configuration: how to hook up different data sources, the various types of track that can be displayed, and the extension of JBrowse via custom code development.

Objectives

Results

Conclusion