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Explore DNA-Seq and RNA-Seq BAM filesGenomeBrowse

GenomeBrowse raises the bar on the experience of exploring and finding key insights into your genomic data. Every component has been designed and optimized to give you a user-experience beyond imagination.

GenomeBrowse is a free product and can be downloaded here:


Download free genome browser




Golden Helix GenomeBrowse® visualization tool is an evolutionary leap in genome browser technology that combines an attractive and informative visual experience with a robust, performance-driven backend. The marriage of these two equally important components results in a product that makes other browsers look like 1980s DOS programs.

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.

Visualization Experience Like Never Before

GenomeBrowse makes the process of exploring DNA-seq and RNA-seq pile-up and coverage data intuitive and powerful. Whether viewing one file or many, an integrated approach is taken to exploring your data in the context of rich annotation tracks.

This experience features:

  • Zooming and navigation controls that are natural as they mimic panning and scrolling actions you are familiar with.
  • Coverage and pile-up views with different modes to highlight mismatches and look for strand bias.
  • Deep, stable stacking algorithms to look at all reads in a pile-up zoom, not just the first 10 or 20.
  • Context-sensitive information by clicking on any feature. See allele frequencies in control databases, functional predictions of a non-synonymous variants, exon positions of genes, or even details of a single sequenced read.
  • A dynamic labeling system which gives optimal detail on annotation features without cluttering the view.
  • The ability to automatically index and compute coverage data on BAM or VCF files in the background.
A heterozygous variant in ERCC6.

Stream Public Annotations Seamlessly via the Cloud

Golden Helix offers a fully-stocked repository of public annotations on the cloud including dbSNP, 1000 Genomes, NHLBI 6500 Exomes, UCSC Known Genes, Ensembl, the OMIM catalog, and much more.

All public annotation tracks are hosted on the cloud with optimized on-demand streaming so that you don’t have to download them to start viewing data. Annotations are updated frequently and automatically by Golden Helix so that you can have immediate access to the most up-to-date information.

Additional species are also available including bovine, canine, ovine, and more.

Validate Variant Calls in Your Sample(s)

GenomeBrowse provides a complete picture of genomic context and read-based evidence to support a variant call so you don't have to wonder if a call is correct. You can quickly spot systematic strand bias, alignment mismatches due to InDels, or issues with nearby read coverage that can produce false-positive variants.

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

Online Support »

Additionally, the search-powered location bar allows you to quickly jump to any area of interest to start an investigation by simply typing in a gene name or genomic coordinates.

Trio Exploration and de Novo Discovery

Analyzing a trio (a father, mother, and child sample set) gives you unique analytic capabilities because inheritance patterns can be examined and evidence of de Novo mutations scrutinized. GenomeBrowse gives you insight into each and every mismatch in the sequence reads to lend confidence to the validity of inheritance patterns. Trios can be further analyzed by comparing data against public annotations of known variants.

Coverage centers around the exons but trails off considerably on the 3' UTR side.

View Local, Network, or EA Pipeline Files

Easily manage repositories of BAM and VCF files, whether they are on local hard drives or network attached storage with an integrated download manager that can be used to create local copies of cloud-based public or private data files.

Further, GenomeBrowse is tightly integrated with the EA Pipeline so that EA customers have immediate streaming access to their RNA-Seq analysis outputs, saving terabytes of data download.

Publication-Ready Visuals

When you are ready to publish, you can create beautiful screenshots to complement your submission. Colors can be customized and a cross-plot anchor can be set to draw attention to the most relevant discoveries.

A trio zoomed to the X chromosome.

Built on the Best Technology

All major platforms are supported with native installers that do not rely on virtual machines and emulators that hog system memory and lack desktop integration. Multi-core enabled performance gives faster rendering and more scalable, detailed visualization than any other genome browser. Compressed, asynchronous streaming of network sources means that you see each plot load quickly without locking up the user interface.

GenomeBrowse integrates with the powerful Golden Helix SNP & Variation Suite (SVS) analysis platform. SVS can be used to build custom annotations and perform variant analysis, while GenomeBrowse can visualize findings and validate the evidence for putative variants.

Free Download Links - Version 1.1.2

     
Preferred if you have a 64-bit OS If you have a 32-bit OS
     
Ubuntu 8.04+ or similar distribution 32-bit Ubuntu 8.04+ or similar RHEL or CentOS 5.x or 6.x Mac OS X 10.6+


Release Notes

Version 1.1.2 - 5/29/2013

  • Added support for reading sorted BED files directly! The "track" line is respected to support display name, coloring and the bedDetail format variant.
  • A new table view of a source's features is available on the top-left of plots when you hover over them. You can view the features based on the current zoom or from the start of the source. Selecting features in this view jumps the zoom to that position.
  • Added more details to the data console output for BAM coverage plots. Percentage of total reads is now an additional column for each nucleotide and insertion detected at the current position.
  • Added an additional option to choose whether to automatically display of Coverage and/or Pile-up plots when adding new BAM sources. If either coverage or the pile-up plot is not displayed automatically, it can be shown by checking the appropriate box in the plot tree view.
  • The "garead" and "gautil" command line utilities are bundled with GenomeBrowse. Running `gautil precompute <source.bam>` will produce index and coverage files. This may be useful for pipeline environments to prepare files for GenomeBrowse visualization.
  • Some glitches with parsing the input to the location bar have been resolved. It has also been improved to be able to take whitespace delimited region descriptions like "chr7 123,456 444,555" as well as many others. As you type, the normalized range that was detected is shown in the results drop down so you know exactly what range will be used when you hit Enter.


Version 1.1.1 - 4/5/2013

  • Overhauled the touch pad input handling on Mac. Zooming is significantly more responsive. Two finger scroll up and down zooms in and out while side to side pans the view.
  • Before registering, you can now open a cloud-based demo project to give GenomeBrowse a test drive.
  • Show transcript names as a hover-label when looking at whole genes.
  • Fixed some crashes and unexpected behavior with the new downloader engine.
  • Fixed issue where you could not log in if the "Stay Logged In" checkbox was not checked.
  • Fix display of data for VCF coverage at chromosome level scale for sparcely populated sources.
  • Reverse-strand hard-clipped reads were not being aligned correctly and thus looked like they had a lot of mismatches.
  • Updated the links for gene names in the data console.


Version 1.1.0 - 3/26/2013

  • Completely new downloader engine that supports download acceleration, pause/resume, auto-resume and can be minimized to the system tray for long downloads.
  • Files are now downloaded with their precomputed coverage or indexes so they are immediately displayable.
  • From pipeline.goldenhelix.com, ghdownload will now open the new GenomeBrowse downloader.
  • Support for VCF Files! New rendering mode for multi-sample "Variant Maps", as well as auto-compression/indexing of VCF to Bgzip/Tabix format required to read files directly for rendering.
  • Single sample VCFs, multi-sample VCFs and even "site"-based VCFs with no sample data are now supported.
  • SNV and InDels supported. We will do our best to draw Structural Variants, but their representation in VCF format is less standardized.
  • GenomeBrowse should now start faster once you have downloaded the reference sequence track for your existing project.
  • We have experimental support for "Value" tracks. More support coming in the near future.
  • Many polishes and bug-fixes, including improved controls for changing labels on features.
  • Gene tracks have been much enhanced. Exon numbers and transcript names are labeled at appropriate zoom levels as well as more details are provided while hovering over codons.
  • The reference sequence track gives you forward, reverse and all theoretical amino acid encodings as you expand its height to give it more space to draw.
  • Improved Y-axis labels, which is especially important when looking at VCF tracks with sample names as Y-axis labels.


Version 1.0.7 - 1/30/2013

  • Added the "g1k" Human Reference build, which is GRCh37 with the rCRS MT as specified by the 1000 genomes project.
  • Updated the genome assembly file format to handle more meta-data. Also improved when warnings are displayed for a source not matching the selected build.
  • Added ability to change the field used to label features for Interval and Variant plots.
  • Polished the label drawing system for all plot types.


Version 1.0.6 - 12/4/2012

  • Added ability to filter low quality alignments from pileups and coverage plots.
  • Polished rendering of BAM plots and mouse-hover capabilities.
  • Performance improvements when rendering views with tens of thousands of reads.
  • Significantly improved "gear" menu and control panel capabilities of plots.
  • Fixed some crashes in pre-compute reported by users.
  • Added an Update Available notification.


Version 1.0.5 - 11/5/2012

  • Add ability to have project documentation.
  • Have "demo" mode for putting on thumb drives.

Version 1.0.4 - 10/30/2012

  • Added project management! Create new projects, save and open recent projects.
  • Multi-window support: can open multiple projects in multiple windows.
  • Added Illumina BaseSpace integration in the 'Add' dialog.
  • Amino-acid information now drawn on genes. Also labeling of gene parts enhanced.
  • Fixed crashes associated with attempting to index or run precompute on an unsorted BAM file.
  • Fixed crashes when precomputing on certain BAM files.
  • Prevent cache system by being overloaded by 30K+ read-depth regions. This should help with out-of-memory errors when viewing areas ultra-high-read-depth.


Version 1.0.3 - 10/1/2012

  • Fixed issue where the directory to store settings and the default project was not created. You should now not need to log in every time you start GenomeBrowse and your project should save on close.
  • The message boxes and progress dialogs have been updated to have a more consistent style.


Version 1.0.2 - 9/19/2012

  • Made the Windows installer able to be run by a non-Administrator user.
  • On Mac, use the native directory chooser so you can pick mounted volumes.
  • Prompt the user to download a reference sequence track if there is not one locally when switching genomes or on first use.


Version 1.0.1 - 9/11/2012

  • Fixed some crashes on Mac OS X when switching to and from GenomeBrowse.
  • Fixed plots that got stuck in "Initializing..." mode.
  • A few fixes of handling views of edge cases.


Version 1.0.0

  • Complete overhaul of the zoom system. Scroll wheel zooming on pile-up beautifully scales the content to an ideal aspect ratio.
  • Login and registration window in place.
  • Improved drag-n-drop of plots by their handles.
  • Per-base quality information is used to shade mismatches in both pile-ups and coverage views.
  • Many tweaks, polish and optimizations.


Version 0.9.9

  • Improved interactive mouse support for insertions. Labels displayed on hover for pileup and coverage plots.
  • Polish and performance improvements to BAM rendering plots.
  • While Y-axis zoom lock is enabled, smoothly adjust the y-limits as you pan into areas with high and low coverage.
  • Significant performance improvement for Mac renderings, and improved handling of touchpad inputs like pinch-zoom and panning.


Version 0.9.8

  • Added interactive mouse support for the labeling system, allow you to hover over genes or variants and see their label even if it was hidden by default.
  • Fixed crash when viewing certain regions of the 1000 Genomes track from our annotation server.
  • Certain types of BAM files were creating invalid BAI files, which is now corrected.
  • Fixed UI freeze that occurred when you tried to delete a plot that had a computation in the queue to be run.


Version 0.9.7

  • Added a paired-end drawing mode to pile-ups! Use the gear menu to access this new drawing mode.
  • Detect sample.bai as valid BAI file instead of just sample.bam.bai.
  • Larger zoom limits in pile-up mode before switching to drawing coverage.


Version 0.9.6

  • Updated logo and name


Version 0.9.5

  • New pipeline.goldenhelix.com account integration. Redesigned the "Add" dialog to have tabs for Annotations, EA Pipeline Account and Example Samples.
  • The Landmark view displays the Cytobands track by default, but can be set manually to show other plots.
  • Totally new labeling system for genes and variant tracks. You'll notice transcripts are grouped by their gene and have labels on the exons and utrs. Genes also collapse transcripts when vertical space is tight.
  • The BAM pile-up plot now has a "gear" icon in the top left that allows you to switch coloring modes to emphasize mismatches versus strands. Also "Split by Strand" stacks forward and reverse strands above and below the X-axis.
  • Tools->Proxy Settings allows you to auto-detect or manually enter proxy settings.
  • Many stylistic improvements and user interface polish and tweaks. 


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