From FASTQ to Clinical Report

We provide a complete, end-to-end solution for clinical labs and hospitals to analyze Next-Generation Sequencing data.


In business for 20 years and cited in 1,300+ publications, we are proud to support over 10,000 users in more than 350 institutions worldwide.


Our entire clinical pipeline consists of software products that are deeply integrated with each other. In addition, we provide automation capabilities that are crucial in high-throughput testing environments.


No per-sample charges! You will save money with our annual subscription model. Licenses include unlimited training and support to ensure success.

Popular Products

SNP & Variation Suite

SNP & Variation Suite is a powerful analytic tool that allows biologists and other researchers to easily perform complex analyses and visualizations on genomic and phenotypic data.

  • GWAS & SNP Analysis
  • Large-N DNA-Seq Analysis
  • Genomic Prediction
  • Copy Number Analysis
  • RNA-Seq Analysis

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VarSeq is an intuitive, integrated software solution for tertiary analysis. With VarSeq you can automate your workflows and analyze variants for gene panels, exomes and whole genomes.

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Built on the same algorithms of Varseq, VSWarehouse is a scalable, multi-project warehouse for NGS variant call sets, clinical reports and catalogs of variant assessments.

  • Fully Integrated with VarSeq Workflows
  • Scalable Technology
  • Organize Samples into Projects
  • Centralized Clinical Report Hosting
  • Create Variant Assessment Catalogs

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Support for Various Industries

Customer Testimonials

Jeffrey Rosefeld, Ph.D

Rutgers Cancer Institute of New Jersey

Dr. Jeffrey Rosenfeld, Bioinformatics Scientist

“Being an informatics person, my job is to set the system up. Now that it’s up and running the molecular pathologist can run the samples. They do not need an informatics person to run every sample.”

Read Rosenfeld's Case Study

Benjamin Darbo, Ph.D

University of Iowa

Dr. Benjamin Darbro, Director of Shivanand R. Patil Cytogenetics and Molecular Laboratory

“VarSeq had everything we were looking for with regards to annotation, filtering sources and an actual visual browser within the software itself. But what really set it apart in retrospect is how intuitive it is.”

Read Darbro's Case Study

Heather Huson, Ph.D

Cornell University

Dr. Heather Huson, Professor of Dairy Cattle Genetics, Odyssey DNA Lab

"The huge benefit of SVS is it's user-friendly and you can basically visualize your results in the same program. You don't have to spend nearly as much time manipulating data and results to get it in the right input and output formats."

Read Huson's Case Study

Hela Azaiez, Ph.D

University of Iowa

Dr. Hela Azaiez, Associate Research Scientist, Molecular Otolaryngology and Renal Research Laboratories

“SVS opened so many doors for my research. It allowed me to explore new ideas. It allowed me to do stuff I never thought was even possible to do in that amount of time, so I could test so many hypotheses. All that I had to do is click a button.”

Read Azaiez's Case Study

Rick Kittles, Ph.D

University of Arizona

Dr. Rick Kittles, Director, Center for Population Genetics

"SVS goes beyond simple genotype associations with Identity By Descent (IBD) calculations, principal component analysis, and the ability to visualize results, all in one application. So when people say 'It costs money,' I say it's better to have one program that can do everything than to look for updates on multiple applications all the time."

Read Kittle's Case Study

Upcoming Webcast

Using the GRCh38 reference assembly for clinical interpretation in VSClinical

Semptember 26, 2018 | 12:00 PM EST

Presented by: Gabe Rudy, VP of Product & Engineering, Golden Helix

Although the latest reference genome (build 38) was released in 2009, it has taken quite a while to come into its own as a baseline for the clinical interpretation of variants in human disease. A lot of this was momentum, while some of it was concerns about compatibility with other labs and published literature. Yet the largest hindrance was the lack of support of the bioinformatic tools and requisite databases required to analyze variants. When we released VSClinical, we wanted those concerns to be removed from the choice of what reference genome a lab may choose to use.  

In this webcast, we will:

  • Review the cost and benefits of using the new GRCh38 reference genome in the context of clinical genetics.
  • Look at the public data resources that have native support, and Golden Helix’s effort to lift over the ones that do not.
  • Provide examples of situations where changing reference genomes introduces or negates artifacts caused by errors in the reference sequence.
  • Demonstrate VarSeq’s new ability to lift over to the new reference genome while importing your VCFs into a project.
  • Go through VSClinical using the new human reference genome, with full annotation support and downstream use of assessment catalogs and writing of reports.

Whether you have already made the switch or considering the possibility, this webcast will provide you with what you need to know about using the new reference genome for clinical genetic testing as well as human disease research using VarSeq. We hope to see you there!