IGV-Web App is a browser-based application for exploring genomic datasets. Developed by the Integrative Genomics Viewer team, it provides an alternative to the desktop application without requiring researchers to install a separate program.
The application is built around igv.js, which provides the underlying visualisation capabilities. Unlike the embeddable library, IGV-Web App offers a complete interface for researchers who simply want to load genomic data and investigate it.
Data can be loaded from local files or remote sources. When working with local files, the application processes the data in the browser rather than uploading it to the hosting server, an important consideration when handling unpublished research data.
This is free and open source software.
Key Features
- Supports reference genomes supplied as FASTA, GenBank or twoBit files, alongside a selection of predefined genome assemblies.
- Displays genomic alignments, sequence variants, gene annotations and other datasets as configurable tracks.
- Accepts data from local files, remote URLs and supported cloud storage services.
- Provides navigation by chromosome coordinates, genomic region, gene name and other recognised identifiers.
- Offers continuous zooming and panning, allowing researchers to move between broad genomic regions and individual bases.
- Displays reference nucleotide sequences when zoomed sufficiently close to the selected region.
- Supports indexed alignment files, including BAM and CRAM, together with variant and annotation formats such as VCF, BED and GFF.
- Allows tracks to be reordered, removed and configured independently.
- Can overlay quantitative data tracks with adjustable transparency to facilitate comparisons.
- Supports predefined track collections and saved browser sessions for returning to particular configurations.
- Can be hosted on a conventional web server using static files, with configurable reference genomes and track registries.
Website: github.com/igvteam/igv-webapp
Support:
Developer: Integrative Genomics Viewer team
License: MIT License
IGV-Web App is written in JavaScript. Learn JavaScript with our recommended free books and free tutorials.
Related Software
| Web-Based Desktop Genome Browsers | |
|---|---|
| Ensembl | Resource for geneticists, molecular biologists and other researchers |
| Genome Browser | Interactively visualize genomic data |
| GDV | Exploration and analysis of eukaryotic RefSeq genome assemblies |
| HiGlass | Explore and compare genomic contact matrices and tracks |
| igv.js | Embeddable genomic visualization |
| NGB | Web-based NGS data viewer |
| JBrowse 2 | Modern React-based genome browser |
| trackplot | Visualize various next-generation sequencing data |
| GIVE | Genomic Interactive Visualization Engine |
| Genoverse | HTML5 scrollable genome browser |
| Epigenome Browser | Visualization, integration and analysis tools for epigenomic datasets |
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