igv.js

igv.js is an embeddable interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team.

Examples

Alignments

GA4GH

Copy number

Multiple regions

More

Quickstart

Installation

igv.js consists of a single javascript file with no external dependencies. Pre-built expanded and minified js files can be downloaded from http://igv.org/web/release. The current release is 2.0.0-rc5.

Alternatively you can install with npm

npm install igv

and source one of the files in node_modules/igv/dist.

To use igv.js include it with a script tag

<script src="igv.min.js/>

or import it as a requirejs module

requirejs(['igv.min'], function (igv) {...} (see examples/igv-require.html)

or import it as an es6 module

import igv from 'igv.esm.min.js' (see examples/igv-esm.html)

Usage

To create an igv.js browser supply a container div and an initial configuration defining the reference genome, initial tracks, and other state to the function igv.createBrowser(div, config).

This function returns a promise for an igv.Browser object which can used to control the browser. An example of a browser on a single alignment track opened at a specific locus:

      var igvDiv = document.getElementById("igv-div");
      var options =
        {
            genome: "hg19",
            locus: "chr8:128,747,267-128,754,546",
            tracks: [
                {
                    type: 'alignment',
                    format: 'bam',
                    url: 'https://data.broadinstitute.org/igvdata/1KG/b37/data/HG02450/alignment/HG02450.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam',
                    name: 'HG02450'
                }
            ]
        };

        igv.createBrowser(igvDiv, options)
                .then(function (browser) {
                    console.log("Created IGV browser");
                })

API

See the Wiki for full documentation of the API.

Development

Requirements

Building igv.js and running the examples require Linux or MacOS. Other Unix environments will probably work but have not been tested.

Windows users can use Cygwin or Windows Subsystem for Linux.

Building

Building igv.js and running the examples requires node.js.

git clone https://github.com/igvteam/igv.js.git
cd igv.js
npm install
npm run grunt

This creates a dist folder with the following files

• igv.js, igv.min.js - ES5 compatible files for script or requirejs imports
• igv.esm.js, igv.esm.min.js -- ES6 module

Tests

To run the tests start an http-server

npm run http-server

Then open http://localhost:8080/test/runTests.html.

Examples

To run the examples start an http-server

npm run http-server

Then open http://localhost:8080/index.html.

License

igv.js is MIT licensed.