About Golden Helix

Running PacBio HiFi Workflows in VSWarehouse 3

Jul 30, 2025

Managing long‑read secondary analysis used to mean wrestling with Cromwell servers, custom compute nodes, and a tangle of WDL files. VSWarehouse 3 removes that burden. Drop your PacBio output into a watched folder, and our platform does the rest: spinning up compute, tracking every task, and handing you fully annotated results…

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Automating Pharmacogenomics Workflows with VSWarehouse 3: From Variants to Clinical Reports

Jul 24, 2025

In our recent webcast, we explored how VSWarehouse 3 streamlines and automates pharmacogenomics workflows, transforming raw NGS data into actionable clinical reports. This blog post recaps the webcast, breaking down each component of the standard pharmacogenomics workflows to demonstrate how laboratories can achieve end-to-end automation in pharmacogenomic (PGx) testing. Breaking…

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Leveraging VarSeq for NGS Quality Control

Jul 24, 2025

A crucial step in any next-generation sequencing (NGS) analysis is quality control, which is essential for confirming the validity of potentially clinically relevant findings before proceeding with any subsequent variant interpretation or reporting. While Golden Helix does not directly provide NGS validation services, our VarSeq software provides robust analysis tools…

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Implementing Data Freedom Practices in Your Genomics Workflows

Jul 17, 2025

In the world of genomics, data ownership and portability are fundamental principles that every researcher and clinician should embrace. With the increasing complexity of genomic datasets and the critical importance of long-term data accessibility, having the ability to export your data in multiple formats is not just convenient, it’s essential.…

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Enhancing Solid Tumor Analysis with Golden Helix CancerKB

Jul 15, 2025

This year, the Golden Helix CancerKB curation team has been hard at work expanding and refining the content that supports cancer variant interpretation and clinical reporting. In addition to staying current with the latest FDA-approved therapies and NCCN Guideline-recommended treatments, the team has taken on a significant new initiative: developing…

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Enhanced Transcript Annotation: HGVS Repeat Notation Support in VarSeq

Jul 10, 2025

At Golden Helix, we’ve supported the HGVS variant nomenclature standard since the very first release of VarSeq. The HGVS standard provides a consistent and precise language for describing sequence variants in the context of gene transcripts and is a critical part of clinical genomics workflows. As with all living standards,…

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The Breakend Catalog Format for VarSeq 3

Jul 8, 2025

New to VarSeq 3 is support for breakend catalogs. Breakends represent the junction points of structural variants, which include complex genomic rearrangements like translocations, inversions, and large deletions that play crucial roles in cancer genomics and rare disease analysis. These catalogs are unique as they must save two genomic positions…

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June 2025 Customer Publications: Variant Classifications for Cancer & HHT

Jun 27, 2025

This month, our team at Golden Helix is proud to highlight a series of standout customer publications demonstrating the real-world impact of next-generation sequencing and variant analysis. Featured articles from June 2025 showcase the power of the VarSeq platform in supporting high-quality research across hereditary and somatic disease. From integrating…

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Deploying VSWarehouse 3 With Ease

Jun 26, 2025

Managing genomic workflows at scale has always required a bit of IT expertise. The reality is, Next Generation Sequencing data is quite large and requires substantial compute resources to process. Clinical labs must carefully plan how to scale their IT resources to match their genomic testing workloads. Some labs prefer…

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Visualizing Base Modifications in Long-Read Alignment Files

Jun 19, 2025

We’re excited to announce a powerful new feature in GenomeBrowse that enhances our support for visualizing long-read sequencing data: the ability to color reads by base modifications, such as DNA methylation, directly from BAM and CRAM alignment files. Long-read sequencing technologies like those from PacBio and Oxford Nanopore have unlocked…

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The CoLoRS Database: Enhancing Your Long-Read Sequencing Analysis

Jun 17, 2025

Here at Golden Helix, we continue to develop top-quality bioinformatic software to support high-throughput clinical next-gen sequencing pipelines, including long-read whole-genome-sequencing (WGS) workflows. WGS long-read technologies like PacBio HiFi and Oxford Nanopore offer improved variant calling for SNVs, Indels, structural variants, tandem repeats and repeat expansions, and epigenetic modifications. Each…

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Evaluation Scripts for Importing Structural Variant Calls

Jun 10, 2025

As comprehensive genomic profiling (CGP) becomes the standard in cancer variant analysis, the scale and complexity of next-generation sequencing (NGS) data continue to grow. It is now commonplace to report on small variants, larger amplifications and deletions, various complex structural variants (fusions or breakends) as well as genomic signatures like…

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Reduce, Reuse, Recycle: Creating Automatable Workflow Templates with VarSeq

Jun 10, 2025

Next-generation sequencing (NGS) data analysis often involves multiple steps from variant annotation, filtering, interpretation, visualization, and report generation. Repeating these steps manually for each new project can be error-prone and inefficient. In clinical and regulated environments, we recognize that consistency is critical. That’s why VarSeq offers robust support for workflow…

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Golden Helix’s 2025 T-Shirt Design Competition 

Jun 10, 2025

Calling all creatives, scientists, and fans of clever wordplay: Golden Helix is thrilled to kick-off the 2025 T-Shirt Design Competition! As we gear up for another exciting conference season, we want to see your witty ideas, genetics puns, and eye-catching graphics.   This year’s winning designs will be unveiled at the…

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Visualization With IGV

Jun 5, 2025

Modern genomics workflows often require multiple specialized tools working in concert. In the upcoming VarSeq release, we are excited to announce the option for tighter integration with IGV. Genomics researchers and clinicians are well-versed in using IGV as a visualization tool for their genomic data. This new option will allow…

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Enhancing Long-Read Alignment Visualization in GenomeBrowse

Jun 3, 2025

Long-read sequencing technologies have opened new doors in genomics research, enabling more comprehensive analysis of structural variants, phasing, and complex genomic regions. To support these powerful applications, we’ve introduced several new features to GenomeBrowse that specifically enhance the visualization of long-read alignment files. These improvements are designed to help our…

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Importing External PGx Calls for Extended Gene-Drug Reporting in VarSeq

May 27, 2025

Pharmacogenomic (PGx) analysis empowers researchers and clinicians to tailor drug therapies based on a patient’s genetic profile, but not all regions of the genome are easy to interpret. Genes like CYP2D6 and HLA-A are tricky when it comes to rendering diplotype calls. This is due to a number of factors…

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Golden Helix Launches Enterprise Genomic Analysis with VarSeq 3 and VSWarehouse 3

May 22, 2025

Today, we announced the release of VarSeq 3 and VSWarehouse 3, marking a major milestone in enterprise-scale secondary and tertiary genomic analysis. The release introduces cloud-native deployment options optimized for AWS and Azure, expanded support for hybrid and on-premise support, flexible licensing models, including per-sample packaging tailored to small and…

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Customized Auto Variant Interpretation in VarSeq

May 15, 2025

The VarSeq platform has been on the market for over a decade and has established itself as robust and powerful clinical-grade bioinformatics software. Its usage spans many types of analysis, including pharmacogenomics, rare disease, hereditary cancer, somatic, carrier risk, and trio/family. Fundamentally, users have the freedom to build any workflow…

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Leveraging ClinVar Curated Databases in VarSeq

May 13, 2025

ClinVar is a global, publicly accessible database maintained by the National Center for Biotechnology Information (NCBI) that archives interpretations of human genetic variants and their clinical relevance. ClinVar consists of contributions from clinical labs, expert panels, and research groups, and serves as a community-powered knowledge base that is foundational for…

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