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.

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

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VSPipeline Tutorials

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VSPipeline in Action

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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

VarSeq is on-premises software, ensuring full control over installation and data management. It is compatible with various deployment environments including workstations, server setups with remote desktop access, and private cloud servers.

The software is optimized for operation within strict corporate firewalls. It seamlessly integrates with existing web proxy configurations, ensuring uninterrupted functionality in secured network infrastructures. VarSeq's internet connectivity requirements are minimal. It only needs to connect to a select group of Golden Helix servers. This connection is essential for license verification and accessing annotation data updates.

See System Requirements for more details of hardware and operating systems requirements based on planned workflows.