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Explore DNA-Seq and RNA-Seq filesGenomeBrowse

The free Golden Helix GenomeBrowse® tool delivers stunning visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an intuitive user interface to make sure that your discovery process is fluid and streamlined.

Download now:

FREE? SERIOUSLY?

Yes, it really is totally 100% free. Forever.

So, what's the catch?

First of all, we think of GenomeBrowse as a way to give back to the genomics community.

Secondly, we simply want more people to know about Golden Helix and our great products and services.

We hope that by using GenomeBrowse, you get a feel for the type of products Golden Helix builds and the company we are, and you will feel confident trying SNP & Variation Suite, our flagship product.

Unparalleled Visualizations

GenomeBrowse focuses on displaying data in a form that helps you quickly and easily understand what the data is saying. Each variant and its surrounding context is displayed in extraordinary detail.

To help you get the most out of your data, GenomeBrowse provides:

  • Multiple coverage and pile-up views that make mismatches stand out.
  • Natural pan and zoom controls that quickly allow you to zero in on a region of interest.
  • Stacking algorithms that provide stable pile-ups so that your genomic context is constant.
  • Customizable color palettes to tailor plots to your data.
  • A smart labeling system that balances clarity with information density.
  • Integrated search and location bar.
  • External links to UCSC, Ensembl and NCBI.
  • Multiple views of the same data source: Feature tables, per-click feature report, multiple plot types per source.
  • Plots that are easily customized with on-plot hover controls and advanced options in a plot-type specific control panel including styling, smoothing, and filtering.

Backed by the Cloud

A large annotation library curated by Golden Helix is available on demand from our servers eliminating the need to waste time downloading gigabytes of files to see if an annotation exists at a specific position. If you need offline access to any annotation, it can also be downloaded.

A heterozygous variant in ERCC6.

Hosted annotations include:

  • ClinVar
  • dbSNP
  • 1000 Genomes
  • dbNSFP
  • SIFT and PolyPhen
  • COSMIC
  • Ensembl Genes
  • RefSeq Genes
  • NHLBI 6500 Exomes
  • Many, many more

If your alignment data is stored in the cloud or an internal network, GenomeBrowse provides the ability to easily stream it when given either the direct URL or the URL to a containing directory.

Support for a Variety of File Formats Including Custom Data Sources

GenomeBrowse is flexible enough to handle a wide variety of file formats. Many formats can be viewed in multiple ways to highlight what is important in the data. Supported formats include:

  • BAM
  • VCF
  • GTF
  • FASTA
  • TSV and CSV
  • 2Bit
  • BED
  • WIG

GenomeBrowse can display data from both NGS and GWAS studies as long as it can be represented in any of our supported formats or convertible with our powerful Convert Wizard. Coverage information is generated automatically and in the background for BAM and VCF files so that you don't have to use a different tool just to view your data.

A wide variety of reference sequences ship with GenomeBrowse including GRCh37 g1k for Humans, Bos taurus, Ovis aries, Gallus gallus, and Baker's yeast. Custom reference sequences can be added for your species using the Convert Wizard which can transform numerous file formats into a GenomeBrowse reference.

HOW IS IT DIFFERENT?

GenomeBrowse is different than other genome browsers on the market:

  1. It's easy to learn and easy to use.
  2. No outside tool is needed to compute coverage or convert file types.
  3. Annotations are hosted on our cloud so you don't need to find/store them yourself.

Gain Confidence in Your Variant Calls

GenomeBrowse displays the raw data the variant caller used to make its decision. You can quickly spot systematic strand bias, alignment mismatches due to InDels, or issues with nearby read coverage that can produce false-positive variants.

Display All Your Samples

Whether you are conducting a case/control study, analyzing a trio, or many independent samples, GenomeBrowse can display all your alignment data. Looking at all your samples in one view can help you spot contextually relevant findings.

  • Do all the cases have a InDel in the same region?
  • Is the child’s mutation actually de Novo or did the variant caller miscall one of the parents?
  • Is the coverage deep enough across all samples?

Now you can have visual confirmation for the above issues and more.

Collaboration Ready with Evernote Integration

GenomeBrowse ships with first-class, native integration with Evernote. You can easily save your genomic findings in GenomeBrowse with bookmarked regions and screenshots to any of your Evernote notebooks. These notes can be shared with colleagues and collaborators so that getting feedback is just a click away. Notes can be tagged and then easily searched, making your GenomeBrowse projects as organized as you want to make them. Read more about the Evernote integration on "Our 2 SNPs..." »

A trio zoomed to the X chromosome.

Automate Your Workflow

GenomeBrowse can be controlled programmatically via HTTP so that you can quickly generate the visualizations that interest you via remote access. Use the built-in automation functionality to integrate GenomeBrowse into your existing workflow with ease and flexibility.

Create High Quality, Print-Ready Visuals

Easily generate publication quality plots that showcases how your data clearly supports your discoveries. Plots are rendered to ensure that your data looks as good in print as it did on screen. All user interface elements that might distract from your data are stripped from the image. Colors are highly customizable and a cross-plot anchor can be set to draw attention to the most relevant discoveries.

Built for Your Computer

Check out our online resources including video tutorials, webcasts, and more!

GenomeBrowse runs as a native desktop application on your computer. No longer do you have to sacrifice speed and interface quality to obtain a consistent cross-platform experience. It was developed with performance in mind to deliver a faster and more fluid browsing experience than any other genome browser available.

GenomeBrowse is also integrated in the powerful Golden Helix SNP & Variation Suite (SVS) analysis platform. If love the visualization experience of GenomeBrowse, check out SVS for filtering, annotating, and analyzing your data prior to utilizing the same visualization interface. Learn more about upgrading from GenomeBrowse to SVS »

Release Notes

Release notes are available in the GenomeBrowse manual.






License Restrictions for Commercial Organizations

Individuals from commercial companies are free to download, install, and use GenomeBrowse inside their organization without any cost or restrictions except the general use restrictions outlined in the End-User License Agreement for GenomeBrowse. If a company is interested in adding GenomeBrowse as a "value add-on" to their product, including but not limited to links within the product to GenomeBrowse and/or full instances of the software, and/or if the organization intends to use GenomeBrowse for any monetary or other business benefit, they must contact Golden Helix at info@goldenhelix.com or 406-585-8137 for a separate licensing agreement.

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