The added value of GenomeBrowse

GenomeBrowser users worldwide

This map indicates countries that have GenomeBrowse users

We released GenomeBrowse 2.0 earlier this year, allowing users to review all types of genomic data. Since then, it has received rave reviews from thousands of users around the world. Essentially, it’s the Google Earth app for genomic data.

GenomeBrowse allows a user to sift through vast amounts of genomic data, and make it easy to focus on a single part or the whole. GenomeBrowse has reached global adoption; as of July 2014 thousands of users worldwide have begun to use this product.

Do you want to review a few hundred genomes on your desktop computer? No problem. We want to make this process as simple and intuitive as possible. Here are some key aspects of GenomeBrowse:

Visualization: It turned out that in order for us to display vast amounts of genetic data, we had to solve a number of difficult user interface issues such as:

  • 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, tailoring plots to your data
  • A smart labeling system that balances clarity with information density
  • Integrated search and location bar
  • 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

 

Annotation library:  Golden Helix has curated a large annotation library that is available on demand from our servers, eliminating the need to 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. Hosted annotations include:

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

 

File Formats: GenomeBrowse can display data from both NGS and GWAS as long as it can be represented in any of our supported file formats. BAM, VCF and BED files can be added and visualized directly, and are automatically compressed and indexed for you if they are not so already. Other formats are convertible with our powerful and self-guided Convert Wizard. To enable seamless navigation from per-base details to chromosome sized features, we automatically compute coverage information for your BAM and VCF files. No need to go out to a command line tool. Here is a list of standard file formats we are supporting:

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

 

Why is this all important?

GenomeBrowse allows researchers to take a look at raw data in a very intuitive way, making it possible to easily find out more about issues such as recognizing strand bias or identifying alignment mismatches due to indels, or identifying read coverage issues.

The tool becomes exponentially more valuable as users employ it in conjunction with SNP & Variation Suite (SVS). After conducting a variant analysis, our users have narrowed down the list of variants to a manageable list of specific loci they are interested in learning more about. Then, the power of GenomeBrowse comes in handy as it allows users to quickly cross reference public and custom databases for a specific variant. Like in Google Earth, we enter a particular street address and are able to take a closer look at a particular house and its neighborhood, GenomeBrowse can very effectively display all available information about a particular locus.

We at Golden Helix are committed to keeping GenomeBrowse free. It’s the first step in gaining a better understanding of genomic data. We see it going forward as a cornerstone of our product stack, as it makes the output of SVS and future analytics products much easier to interpret.

One thought on “The added value of GenomeBrowse

  1. Pingback: VarSeq: Making Variant Discovery and Gene Panels Easy | Our 2 SNPs…®

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