igv.js
3.0.8
igv.js is an embeddable interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team.
James T Robinson, Helga Thorvaldsdottir, Douglass Turner, Jill P Mesirov, igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV), Bioinformatics, Volume 39, Issue 1, January 2023, btac830, https://doi.org/10.1093/bioinformatics/btac830
Below are examples and a quickstart guide. See the developer documentation for more documentation.
Alignments
Interactions
Copy number
Multiple regions
Mutation Annotation Format (MAF)
Variant color options
More
igv.js consists of a single javascript file with no external dependencies.
Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js) can be downloaded from https://cdn.jsdelivr.net/npm/[email protected]/dist/.
To import igv as an ES6 module
import igv from "https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.esm.min.js"
Or as a script include (defines the "igv" global)
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 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");
})Full documentation of the igv.js API is available at https://igv.org/doc/igvjs/.
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 - 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 (ES6).
igv.js is MIT licensed.
