Repeatable clinical workflows essential for CLIA and CAP certified analysis, creation of high throughput pipelines and access to curated annotation sources that are updated regularly.


Up-to-Date Annotations

VarSeq provides access to a wide selection of public databases which Golden Helix curates and updates for our customers on a quarterly basis. The annotation and curation process ensures that the data is high quality and will work with your imported variants. While the current versions of these databases are always available, past versions are also accessible. The specific annotations used in your analysis are stored locally with your data and are never changed without your explicit request. This ensures that your analysis is performed on a stable dataset and your results are reproducible and available in the future.

Power and Flexibility for High Throughput Environments

Working in a high throughput environment requires increased power and flexibility, and VSPipeline delivers. The command line runner provides you access to the full power of VarSeq's algorithms and flexible project template system from any command line context, including your existing bioinformatics pipeline. Along with fully computed VarSeq projects, VSPipeline can also be used to generate other deliverables such as annotated text or VCF files as well as multi-tab Excel reports of filtered variants, sample and coverage regions statistics.

Repeatable Clinical Workflows

VSPipeline allows you to create workflow-encoded project templates which lock down quality control and filtering parameters, automating your pipeline and providing you with the requirements needed for CLIA and CAP certified analysis. The VarSeq® project produced by the automated pipeline can be opened and used by the lab staff to complete the variant interpretation and reporting using the easy-to-use graphical interface.

Built for Clinical Settings

VSPipeline was built with our clinical users in mind, and it will prove beneficial in all clinical settings where there is a need to automate the testing pipeline, including labs conducting cancer and hereditary gene panel testing, as well as those analyzing whole exome and whole genome sequencing data. In addition to clinical users, bioinformatics core labs can leverage the fast and flexible annotation algorithms in VarSeq and Golden Helix's unmatched and up-to-date public annotation repository with VSPipeline.


Since GenomeBrowse is built into VarSeq, it is easy to verify coverage across your amplicons. Simply add your BAM and BED files to your project and inspect the pileups directly. GenomeBrowse provides the context you need to have confidence that your upstream sequencing pipeline is working correctly.

Use Cases

VSPipeline is a command-line interface that will provide high throughput environments the ability to tap the full power of VarSeq’s algorithms and flexible project template system from any command line context, including existing bioinformatics pipeline.

So, what is the big deal? Here are the top three most important aspects of this new product:

1. Repeatable Workflows

For our users in CLIA and CAP certified labs, it’s a convenient way to lock down a workflow that has been designed in VarSeq. Once this task has been accomplished, this workflow (e.g. a gene panel or a specific whole exome workflow) can be automated. This further the reduces the chance of any human error.

2. Performance

Labs that are dealing with an increasing number of samples are able to achieve higher throughput by automating their entire pipeline from FastQ to final report. VSPipeline enables bioinformatic cores to automate the entire tertiary analysis process – saving time and allowing labs to scale to higher demands.

3. Curated annotation tracks

At Golden Helix, we spend a lot of time to get the little things right. We ship VarSeq and VSPipeline with a number of curated annotation sources, such as dbSNP, ClinVar and CIViC (just to name a few). Data curation can be a hassle; it’s time consuming and expensive for a lab to do on their own. However, our careful curation process will ensure that you have the highest quality data and take the hassle out of your hands.

VarSeq has been very well received by our clinical users and has provided them with immediate impact. Now, VSPipeline becomes key to scale up precision medicine.

Case Studies

We know our software will exceed your expectations. But don't just take it from us, see how our customers have benefitted from it.

Recommended Learning Materials

We have a variety of supplemental learning materials that are an excellent resource for anyone interested in the industry or our software solutions. Here are some of our recommended materials for you to check out related to VSPipeline!


Check out our free eBooks on a variety of different topics:


Watch how to use clinical reports as part of a Gene Panel Pipeline.

Using Clinical Reports as part of a Gene Panel Pipeline

Other Resources

Explore a clinical workflow in VarSeq or follow along with a tutorial!

VarSeq Viewer

Download Here

VSPipeline Tutorials

View Here

VSPipeline in Action

Download Here

Try VSPipeline for Free

Did you know we offer complimentary trials of our software? No restricted features, no sample data - you get to try all the features of VSPipeline with your data and see how it works!

If you are interested in a trial, please fill out the form below, and we will send you the details!

Technical Specifications


4 GB of RAM

Multicore CPU

100GB of space available for annotations and projects


If you are working with whole exomes or genomes, especially if or hundreds to thousands of samples, we suggest a high-memory configuration and plenty of storage capacity:

16GB+ of RAM (32GB for Servers)

8+ CPU Cores

1TB of space available for annotations and projects


The following operating systems are supported:

64-bit Windows 7 or later

Linux Ubuntu 14.04 or later (64-bit only)

Linux RHEL 7 or later, or equivalently CentOS 7 or later (64-bit only)

Mac OS X 10.11 or later


With a server license, you can install your Golden Helix software solution on a server with multi-user access and shared resources. You can launch any number of instances of the software on the same host, and are only limited by the natural CPU, Memory and Disk resources of the server.

For Windows, you would need to use ability for multi-user Remote Desktop only available on Windows Server. We support Windows Server 2008 or newer.

On Linux, clients can log in from any operating system using SSH and open the Golden Helix software using X11-tunneling to interact with the software. On windows, we suggest a solution like MobaXterm that provides a all-in-one SSH client and X11 server to enable easy logging in, file transfer and opening of remote GUI applications.


Golden Helix VarSeq and SVS can be configured to access the internet through a SOCKS5 or HTTP/HTTPS Tunneling Proxy. Go to Tools -> Proxy Settings… to configure.

The software only needs to make outgoing connections on standard HTTP/HTTPS ports and protocols. If a local firewall is installed that prevents these types of outgoing connections (this is very uncommon), firewall rules will need to be created to whitelist the software.

Note we have run into numerous issues where aggressive anti-virus programs prevent the product from performing normal operations such as opening files and logging in. You may need to whitelist Golden Helix executables or disable these tools to perform your analytics.