Integrated Genome Browser (IGB) is a fast, free, and highly customizable genome browser you can use to view and explore big genomic datasets. It lets you view biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
IGB runs on your desktop and can load data from your local files and also from the internet.
IGB is built on top of the Genoviz SDK, a Java library that implements key visualization features such as dynamic, real-time zooming and scrolling through a genomic map, a feature of the IGB browser that sets it apart from many similar tools.
Key Features
- View your RNA-Seq, ChIP-chip or ChIP-seq data alongside genome annotations and sequence.
- Investigate alternative splicing, regulation of gene expression, epigenetic modifications of DNA, and other genome-scale questions.
- View results from aligning short-read sequences onto a target genome, identify SNPs, and check alignment quality.
- Copy and paste genomic sequences for further analysis into other tools, such as primer design and promoter analysis tools.
- Create high-quality images for publication in a variety of formats.
- Animated zooming. Most genome browsers implement “jump zooming” only, in which you click a zoom button (or other type of control) and then wait for the display to re-draw. In IGB, zooming is animated, allowing you to easily and quickly adjust the zoom level as needed without losing track of your location.
- Simple Data Sharing System – QuickLoad. IGB implements a very simple, easy-to-use system for sharing data called QuickLoad. You can use the QuickLoad system to set up a Web site you can use to share your data with colleagues, reviewers, and the public.
- Draggable graphs. You can display genome graphs data (e.g., “bar” and “wiggle” files) alongside and even on top of reference genome annotations, thus making it easier to see how your experimental results match up to the published reference genome annotations. You can reset your graphs to “floating” and click-drag them over annotations to compare your results with annotations and others’ experiments.
- Edge-matching across tracks. When you click an item in the display, the edges of other items in the same or different tracks with identical boundaries light up, highlighting interesting similarities or differences across gene models, sequence reads, or other features.
- Integration with local and remote external data sources. IGB can load data from a variety of sources, including Distributed Annotation Servers, QuickLoad servers, ordinary Web sites, and local files.
- Intron-trimming sliced view. In many species, introns are huge when compared to the exonic (coding) regions of genes. IGB provides a Sliced View tab that trims uninformative regions from introns.
- Web-controls. IGB can be controlled from a web browser or any other program capable of sending HTTP requests. Via IGB links, you can create Web pages that direct IGB to scroll to a specific region and load data sets from local files or servers.
- Scripting. IGB understands a simple command language that allows users to write simple scripts directing IGB to show a genome, zoom and scroll to specific regions, and other functions.
- Open source. All development on IGB proceeds via a 100% open source model. The license allows developers to incorporate IGB (and its components) into new applications.
Website: bioviz.org
Support: User’s Guide
Developer: IGB team
License: Atlassian Confluence Open Source Project License
IGB is written in Java. Learn Java with our recommended free books and free tutorials.
Related Software
| Desktop Genome Browsers | |
|---|---|
| IGV | High-performance visualization genome browser tool |
| IGB | Integrated Genome Browser |
| JBrowse | Fast, scalable genome browser |
| Tablet | Graphical viewer for sequence assemblies and alignments |
| UGENE | Set of integrated bioinformatics software |
| Artemis | Genome viewer and annotation tool |
| Apollo | Instantaneous, collaborative genomic annotation editor |
| SeqMonk | Visualise and analyse high throughput mapped sequence data |
| GW | Fast browser for genomic sequencing data |
| CutePeaks | Cross platform Sanger Trace file viewer |
| ASCIIGenome | Text only genome browser |
| Genome Workbench | Integrated tools for studying and analyzing genetic data |
Read our verdict in the software roundup.
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