Tag Archives: NGS

Automating & Standardizing Your NGS Workflow: Part IV

We have covered a lot of ground in this Automating & Standardizing Your Workflows blog series. First, we saw how to perform secondary analysis with Sentieon to generate the necessary VCF and BAM files for tertiary analysis in Part I. The implementation of VSPipeline allowed for rapid import and project generation for a predefined cancer gene panel project template in… Read more »

Automating & Standardizing Your NGS Workflow: Part III

In our last part of this series, we showed how to run a pre-built workflow template via VSPipeline to automatically import and filter sample variants to streamline the search for clinically relevant variants. Now, we can deep-dive into our filtered, pathogenic variants to fully understand and capture their final classification and interpretation. Filtered Germline Variants for ACMG Guidelines The VSPipeline… Read more »

Automating & Standardizing Your NGS Workflow: Part II

VSPipeline: Automating your Tertiary Workflows The first part of this “Automating & Standardizing your NGS Workflow” blog series covered the secondary analysis steps of read alignment and variant calling with Sentieon. The next step is to transition into the tertiary analysis via utilization of our workflow automation tool, VSPipeline. VSPipeline operates as a command-line tool meant to simplify the deployment… Read more »

Automating & Standardizing Your NGS Workflow: Part I

Secondary Analysis with Sentieon: Rapid and Accurate Variant Calling This blog post will cover the utilization of secondary analysis tools to produce a list of high-quality variants and associated coverage data. This data will serve as the main, importable content for the tertiary stage of analysis where variants are interpreted and classified for their impact on a patients’ disorder. We… Read more »

Automating & Standardizing Your NGS Workflow

As our regular customers may know, we write our blogs to provide relevant content to any NGS-based analysis with VarSeq. Our goal here at Golden Helix is to provide top quality software and guidance on how to use the software efficiently to perform variant analysis. However, this blog series will take a more general perspective and supply some insight into… Read more »

Golden Helix Receives NIH-SBIR Phase 2 Grant 2R44 GM128485-02

Golden Helix, Inc. has announced themselves as the recipient of an NIH SBIR Grant 2R44GM128485-02 entitled “Automated and Guided Workflows for Clinical Testing Using NGS Assays.” “With the help of this grant, we will take the clinical automation of NGS data to the next level, focusing on germline diseases and cancer diagnostics,” states Andreas Scherer, Ph.D., President, and CEO of… Read more »

Secondary Analysis 2.0 – Part V

Detection of CNVs

An Example of an Integrated Clinical Workflow for CNVs and SNVs In this blog series, I discuss the architecture of a state of the art secondary pipeline that is able to detect single nucleotide variations (SNVs) and copy number variations (CNVs) in one test leveraging next-gen sequencing. In Part I, we reviewed genetic variation in humans and looked at the key… Read more »

Don’t miss the VarSeq user experience webcast tomorrow!

We are shortly approaching the public launch (November 5th!) of our first clinical product, VarSeq. We could not have predicted how well the market would accept VarSeq – but we couldn’t be happier! For those of you who have not yet seen our newest product in action, I invite you to register for tomorrow’s webcast: The Golden Helix VarSeq User Experience.

VarSeq: Making Variant Discovery and Gene Panels Easy

Last week, our CEO Andreas Scherer announced our entrance into the clinical testing market with VarSeq. This week, I will be giving a webcast on Wednesday introducing this new tool and demonstrating its capabilities. (Register for the webcast) VarSeq’s focused purpose is making NGS gene testing and variant discovery efficient, scalable and accessible to users with a broad range of backgrounds and specialties. In this blog post, we will examine the use cases that VarSeq supports in more detail,… Read more »

Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying it was only 65 years from lift off at Kitty Hawk to the landing of a man on the moon…. Read more »

Top 5 Webcasts to Watch at GoldenHelix.com

Genomic research is exploding. There is a plethora of new methods and workflows for research and clinical use. While we are a software company at heart, we find ourselves in the role of educators. Our customer interactions are about informing, teaching, and consulting. A few years back, we started with regular webcasts that took this idea to the next level…. Read more »

Leveraging SVS for NGS Workflows

Over the last decade, DNA sequencing has made vast technological improvements. With the cost of sequencing decreasing significantly, sequencing technology has become a product for the masses. The sequencing technology and programs that were once used exclusively by major research institutions are now becoming available in many research facilities around the globe. These tools produce large amounts of data sets… Read more »

The State of NGS Variant Calling: DON’T PANIC!!

I’m a believer in the signal. Whole genomes and exomes have lots of signal. Man, is it cool to look at a pile-up and see a mutation as clear as day that you arrived at after filtering through hundreds of thousands or even millions of candidates. When these signals sit right in the genomic “sweet spot” of mappable regions with… Read more »