igv.js is an embeddable interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team.
Below are examples and a quickstart guide.
See the Wiki for more documentation.
igv.js consists of a single javascript file with no external dependencies. To link directly to the current release copy this snippet
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.min.js"></script>Pre-built expanded and minified js files for ES5 (igv.js, igv.min.js) and ES6 (igv.esm.js, igv.esm.min.js) can be downloaded from https://igv.org/web/release/2.1.0/dist/.
Alternatively you can install with npm
npm install igv
and source the appropriate file for your module system (igv.min.js or igv.esm.min.js) 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)
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");
})
For more details see the Wiki for full documentation of the API.
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 Windows Subsystem for Linux.
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
To run the tests from the command line
grunt test
To run the tests in a browser start an http-server
npm run http-server
Then open http://localhost:8080/test/runTests.html.
To run the examples start an http-server
npm run http-server
Then open http://localhost:8080/index.html.
igv-webapp and igv.js require a modern web browser with support for Javascript ECMAScript 2015. We test on the latest versions of Chrome, Safari, Firefox, and Edge. Internet Explorer (IE) is not supported.
igv.js is MIT licensed.