VarSeq Suite

VarSeq Suite — Clinical Genomics Software

The central platform for clinical variant analysis, interpretation, and reporting. Automate your NGS workflows from raw VCF to signed clinical reports backed by an ISO 13485-certified quality management system.

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ISO 13485 Certified QMS
CE Marked (IVDR)

Clinical genomics software is the foundational technology that enables diagnostic laboratories to transform massive amounts of sequencing data into actionable medical insights. It bridges the gap between raw genetic variants and clinical decisions, providing the tools necessary for rigorous classification, interpretation, and reporting.

As NGS testing scales from targeted panels to whole genomes, the need for a unified variant analysis software becomes critical. Laboratories require a platform that not only automates repetitive tasks but also ensures compliance with evolving standards like the ACMG and AMP guidelines.

The VarSeq Suite stands as the industry-leading NGS interpretation platform, offering an end-to-end solution for tertiary analysis. By integrating curated annotations, real-time filter chains, and guided clinical workflows, VarSeq empowers labs to deliver high-quality results with unmatched efficiency and control.

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What Is Clinical Genomics Software?

Clinical genomics software refers to specialized platforms designed to handle the complexity of human genetic data in a regulated environment. Unlike research-only tools, these systems prioritize:

  • Reproducibility: Ensuring that every analysis can be audited and repeated with identical results.
  • Curated Evidence: Integrating population frequencies, functional predictions, and literature into a single view.
  • Regulatory Alignment: ISO 13485–Certified QMS; VarSeq Dx is CE marked under IVDR 2017/746 for in vitro diagnostic use in the European Economic Area. Designed to support CAP and CLIA requirements.

Why Clinical Genomics Software Matters

The primary goal of using a professional NGS interpretation platform is to maximize diagnostic yield while minimizing turnaround time and operational risk.

  • Operational Scale: Automate the filtering of thousands of variants to find the few that truly matter for the patient.
  • Patient Safety: Reduce human error through standardized workflows and automated evidence gathering.
  • Knowledge Retention: Build a lab-specific knowledgebase of variant assessments that grows with every sample processed.

What to Look for in Clinical Variant Analysis Software

Automation Capabilities

The software should support full automation from FASTQ/VCF import to report generation without losing clinical oversight.

Annotation Quality

Look for platforms that offer monthly curated updates to ClinVar, gnomAD, and other essential genomic catalogs.

Flexible Deployment

Maintain full data sovereignty with on-premises, private cloud, or air-gapped deployment options that you control.

Regulatory & Quality Framework

Verify that the vendor has an ISO 13485-certified quality management system and supports the needs of CAP/CLIA validated laboratories.

Full Spectrum Variants

A single platform should handle SNVs, Indels, CNVs, SVs, and pharmacogenomic star alleles across panels to genomes.

Audit Readiness

Built-in versioning and state saving ensure every clinical decision is tracked and reproducible for years to come.

How VarSeq Suite Supports Clinical Genomics

VarSeq Suite is designed to meet every criterion for clinical excellence. By unifying the entire analytical process, it eliminates the inefficiencies and risks associated with fragmented toolsets.

ISO 13485 Quality

Built under a certified quality management system, VarSeq Dx is CE marked under IVDR 2017/746 for in vitro diagnostic use. Installation verification and tiered proficiency certification ensure clinical readiness.

Curated Annotations

Automatically enriched with monthly curated data from ClinVar, gnomAD, and premium sources like Golden Helix CancerKB™, OMIM, LOVD, and Genomenon.

Automated Workflows

Scale your laboratory operations with VSPipeline, enabling hands-off analysis from sequencer output to clinical report.

Comprehensive Capabilities
Annotation
Transcript Impact
Annotation
Splice Site Prediction
Algorithm
Cohort Allele Frequencies
Algorithm
PGx Star Allele Caller
Automation
ACMG Auto Classifier
Automation
Oncogenicity Classifier
Analysis
Phenotype Gene Ranking
Analysis
Disorder Gene Panels
Inheritance
Compound Het
Inheritance
de Novo Analysis

The VarSeq Clinical Analysis Workflow

1

Import & Annotate

Load VCF or FASTQ data. VarSeq automatically enriches variants with the latest clinical and population annotations.

2

Filter & Prioritize

Apply real-time filter chains with nested logic and phenotype-driven prioritization to surface the most relevant findings fast.

3

Interpret & Classify

Guided ACMG/AMP workflows in VSClinical automate criteria scoring and evidence gathering for final classification.

4

Report & Sign-out

Generate structured clinical reports and archive assessments in VSWarehouse for longitudinal tracking.

A Unified Platform for All Clinical Needs

Explore the core capabilities of the VarSeq Suite, from specialized variant analysis to end-to-end automation.

Variant Analysis

Real-time filter chains with nested logic, curated annotations, and phenotype-driven prioritization.

Clinical Interpretation

Guided ACMG/AMP classification with automated criteria recommendation.

CNV & Structural Variants

Full-spectrum CNV, breakend, fusion, and tandem repeat detection and reporting.

Pharmacogenomics

PGx star allele calling and diplotype determination with CPIC guidelines.

Workflow Automation

Scale your laboratory with high-throughput VSPipeline automation.

VSWarehouse

Enterprise data management and longitudinal tracking of variant assessments.

Broad Spectrum Clinical Applications

Precision Oncology

Automate the interpretation of somatic variants using AMP guidelines, integrating therapy matching and clinical trial search.

Explore Oncology Solutions

Rare Disease Diagnosis

Support for trio and extended family analysis with de novo, compound het, and phenotype-based variant prioritization.

Explore Germline Solutions

Carrier Screening

Partner-paired workflows for reproductive risk analysis, supporting autosomal and X-linked recessive disorder screening.

Explore Prenatal Solutions

Clinical-Grade Reliability and Trust

Golden Helix software is used by over 400 institutions worldwide, from small diagnostic labs to national genome centers.

  • ISO 13485:2016: Our development process is certified to meet the highest standards for medical device software.
  • On-Premises Security: Run air-gapped or in your private cloud—patient data never leaves your infrastructure.
  • Global Adoption: Trusted for routine diagnostics in over 50 countries across germline and somatic testing.

Supporting Platform Capabilities

Sentieon
Secondary Analysis & Alignment
Genomenon Mastermind
Curated Evidence Integration
Premium Annotations
Golden Helix CancerKB™, OMIM, LOVD & CADD
Flexible Deployment
Cloud, On-Premise & Air-Gapped
Security & Compliance
ISO 13485 & CAP/CLIA Readiness
Integrations & API
Connect with LIMS, EMR & EHR

Frequently Asked Questions

Is VarSeq suitable for whole-exome and whole-genome analysis?

Yes. VarSeq is optimized to handle large-scale datasets, providing high-performance filtering and phenotype-driven prioritization that surafces clinically relevant variants across WES and WGS samples.

How often are the annotation sources updated?

Golden Helix provides monthly curated updates to all major annotation sources, including ClinVar, gnomAD, OMIM, and hundreds of others, ensuring your analysis is based on the most current data.

Does VarSeq support both germline and somatic workflows?

Absolutely. VarSeq provides dedicated workflows and guided clinical interpretation for both germline (ACMG) and somatic (AMP) variants within a single integrated platform.

Does VarSeq support both short-read and long-read sequencing data?

Yes. VarSeq natively supports short-read data from Illumina and long-read data from PacBio and Oxford Nanopore. Through our partnership with PacBio, VarSeq delivers optimized workflows for long-read variant calling, structural variant detection, and tandem repeat analysis — helping resolve complex genomic regions that short-read platforms miss.

What types of studies and sample configurations does VarSeq support?

VarSeq is built to handle a wide range of study designs. Analyze single proband samples, parent-child trios, and extended pedigrees for rare disease diagnosis. Run carrier screening with partner-paired workflows. Perform cohort studies with population-level filtering and shared variant assessment. Whether you're running a targeted gene panel, clinical exome, or whole genome, VarSeq adapts to your sample configuration.

Can VarSeq be deployed on-premises?

Yes. VarSeq is designed to run on your local infrastructure or private cloud, providing complete data sovereignty. We also support fully air-gapped environments for maximum security.

VarSeq Insights & Webcasts

Learn how to optimize your clinical NGS workflows with expert-led webinars and articles.

Featured Articles

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On-Demand Webcasts

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ISO 13485 Certified QMS