Introduction
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What is JBrowse 2
JBrowse 2 is a pluggable open-source platform for visualizing and integrating biological data. At its core, it is a genome browser, but it has also been built as an extensible platform to enable visualization of all kinds of biological data.
For those of you who have used the original JBrowse, you'll recognize many of the ideas and use cases JBrowse 2 was built around. JBrowse 2 is a complete rewrite of the original JBrowse, however, and so there are some differences. We hope that you will see that these differences, along with the modern web technologies that power JBrowse 2, enable JBrowse 2 to be an even more flexible and useful tool.
What does it mean to embed JBrowse 2?
JBrowse 2 is built around the idea of componentization, meaning that the different pieces that are developed can be re-used to create different final products. Our full web app, called JBrowse Web, can show not only traditional linear genome browser views, but can also show Circos-style circular plots, dotplots, comparative view, and more. It can also display multiple views simultaneously.
Today we'll be using JBrowse Linear View, which has a subset of features of the full app. It can display a single linear view, which is the most common mode of genome visualization. Where JBrowse Web is a full-page web app, though, JBrowse Linear View is designed to work within an existing web page. You can easily add one or several of them to a page without the use of iframes, and control and react to each instance.