Search results for “VSPipeline”

Using VSPipeline to Automate Tertiary Analysis in VSWarehouse

Sep 17, 2025

In this blog post, I’ll highlight the benefits of using VSPipeline to automate tertiary analysis in VSWarehouse. Users can now run VSPipeline project creation as a standalone task or a final step in a bioinformatic workflow without writing code. Simply use one of our shipped VarSeq projects or create your…

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Evaluation scripts in VSPipeline: We heard you like automation…

Sep 12, 2023

…so we added some automation to your automation so you can automate while you automate! Automation has been a hot topic recently and for all the right reasons. As we (proudly) watch our customers increase their sample and data volume, we are constantly seeking to provide tools to reduce click…

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Running VSPipeline from a Docker Container

Nov 10, 2021

As a lab or group scales the number of NGS samples analyzed, it is important to automate the sample analysis pipeline from the sequencer to the point where it is ready for a variant scientist or lab personnel to follow the interpretation workflow and draft a clinical report. VSPipeline leverages…

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VSPipeline Best Practices

Jun 17, 2021

VSPipeline is becoming a very popular tool among VarSeq users as it is essential for creating repeatable clinical workflows that can be executed in automated fashion. Since VSPipeline is a command-line tool, I think it would be helpful to discuss some of the best practices along with helpful tips for getting the most out of VSPipeline.   Some of you may be less familiar with VSPipeline, so I want to cover how to set up the first…

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Importing CNVs using VSPipeline

Jun 2, 2021

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 the existing bioinformatics pipeline. This feature is a great resource for analyzing large sample volumes as it automates importing…

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VSPipeline Tips and Tricks

Jun 2, 2016

The power of VSPipeline is in it’s ability to automate VarSeq workflows. Using VarSeq to create a pipeline template is great because it allows you to dial in the applied filters as well as interactively organize the annotations and applied algorithms. Automating a workflow with VSPipeline is  straightforward when beginning…

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Fulgent Diagnostics Implements VSPipeline to Speed Analysis & Interpretation

Jul 22, 2015

Today, we are proud to announce our collaboration with Fulgent Genetics, a CLIA certified molecular diagnostics lab. Fulgent offers more than 4,000 single gene tests among others and will implement VSPipeline to help speed up their analysis and interpretation process. On our quest to enable precision medicine, we look forward…

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Top 5 things you need to know about VSPipeline

Jul 14, 2015

Recently, Golden Helix, Inc. announced the addition of VSPipeline to our VarSeq software suite. VSPipeline is a command-line interface that will allow 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,…

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Reducing Cervical Cancer NGS Turnaround Time with VarSeq

Jan 20, 2026

When it comes to cervical cancer, early detection and timely analysis can literally be life-saving. Cervical cancer is the fourth most common cancer in women worldwide, with an estimated 660,000 new cases and around 350,000 deaths each year. Early detection through screening and quick diagnostic support drastically improves outcomes because,…

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Considering Data Quality: From Sequencing to Reporting

Dec 11, 2025

When quality metrics generated during secondary analysis are not incorporated into interpretation and reporting, variants are reported without the important context that could affect confidence in the call. The Golden Helix software suite has been designed to help you bring in quality metrics from secondary analysis through to interpretation and…

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Challenging Genomic Regions: Paraphase Integration in VSWarehouse 3

Dec 9, 2025

Short-read sequencing often fails to capture clinically actionable information from challenging genomic regions. While long-read sequencing now enables accurate and comprehensive detection of complex variants, there are still regions of the genome that remain notoriously difficult to analyze. Unfortunately, many of these regions contain genes that are highly relevant to…

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October 2025 | Customer Publications: Driving Genomic Innovation with VarSeq

Oct 28, 2025

At Golden Helix, we’re proud to see how researchers worldwide continue using our software to accelerate discovery and improve clinical decision-making. These October 2025 publications highlight how VarSeq is advancing genetic research across cancer, hereditary disease, and molecular diagnostics. From identifying new variant mechanisms to expanding our understanding of genotype–phenotype…

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Clinical Variant Interpretation at Scale: Reflections from ASHG 2025

Oct 27, 2025

Recently, Golden Helix attended the ASHG 2025 conference, where we had the opportunity to showcase our partnership with Genomenon. This collaboration took center stage at both our booth and Genomenon’s CoLab session, Automating Genomic Workflows: Cutting Interpretation Time, Accelerating Turnaround, and Increasing Diagnostic Yield. Our discussions centered on a problem…

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October Webcast: Scaling NGS Analysis into Institutional Knowledge with VSWarehouse

Oct 24, 2025

As Next-Generation Sequencing (NGS) becomes central to modern clinical diagnostics, laboratories are managing more data than ever before, and turning that data into actionable insight requires both precision and scalability. In our recent webcast, Next-Gen Sequencing at Scale: Transforming Per-Sample Outcomes into Institutional Knowledge with VSWarehouse, we explored how Golden…

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Reporting Short Tandem Repeats in VarSeq

Sep 30, 2025

Short Tandem Repeats (STRs) are increasingly recognized as clinically important genetic variants, contributing to a wide range of rare inherited disorders. Historically, the analysis and clinical reporting of STRs have been challenging due to limitations in both sequencing technologies and interpretation frameworks. With the advent of long-read sequencing technologies and…

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August 2025 Customer Publications: Applications in Cancer, Prenatal Testing & Rare Disease

Aug 26, 2025

At Golden Helix, we get to see firsthand how our software enables groundbreaking research around the world. Our tools are central to real-world discoveries, from cancer studies and prenatal diagnostics to uncovering new genetic links in rare diseases. These publications from August 2025 showcase how VarSeq and VSPipeline are helping…

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5 Things I Wish I Knew When Getting Started With VarSeq

Aug 7, 2025

As a new member of Golden Helix’s Field Application Services team, I’ve recently been diving into the capabilities of VarSeq and our broader software suite – an experience every new VarSeq user goes through. If I could schedule a training call with my former self, there are some key points…

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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 Carrier Screening Analysis Using VarSeq

May 8, 2025

VarSeq, when used with VSPipeline, automates carrier screening analysis, allowing labs to run them in a parallelized, economical fashion.

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Webcast Follow-Up: Powering Genomic Workflows with Upgraded Catalogs in VSWarehouse and VarSeq 3

Apr 24, 2025

Thank you to everyone who joined our recent webcast, “Powering Genomic Workflows with Upgraded Catalogs in VSWarehouse and VarSeq 3,” presented by Gabe Rudy on April 23rd, 2025. We appreciate the engagement and interest in the latest advancements to our platform. For those who missed it or need a recap,…

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