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.
Mutation Annotation Format (MAF)
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 files for ES5 (igv.min.js) and ES6 (igv.esm.min.js) can be downloaded from https://cdn.jsdelivr.net/npm/[email protected]/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. For example, to open a browser on a single alignment track opened at a specific locus:
var igvDiv = document.getElementById("igv-div");
var options =
{
genome: "hg38",
locus: "chr8:127,736,588-127,739,371",
tracks: [
{
"name": "HG00103",
"url": "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram",
"indexURL": "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram.crai",
"format": "cram"
}
]
};
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 build
This creates a dist folder with the following files
- igv.js - ES5 compatible UMDS file for script include, AMD, or CJS modules. A script include will define an "igv" global.
- igv.min.js - minified version of igv.js
- igv.esm.js -- ES6 module
- igv.esm.min.js -- minified version of igv.esm.js
To run the tests from the command line
npm run test
To run the examples install http-server.
Start http-server from the project root directory
npx http-server Then open http://localhost:8080/examples in a web browser.
igv.js require a modern web browser with support for Javascript ECMAScript 2015.
igv.js is MIT licensed.