Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution

         February 16, 2023

Discover the Thrilling Automation Capabilities of VarSeq Suite for NGS Testing and Learn How We’re Tackling Contemporary Lab Challenges

First off, I’d like to thank everyone who joined us for our February webcast on the automation capabilities of the VarSeq software suite through VSPipeline. For those of you who joined us, I’m sure it’s obvious that automation is a topic that gets our gears turning, but for those of you just tuning in now, I’ll happily repeat myself: the current state of NGS testing automation in VarSeq is absolutely thrilling. During our webcast, Gabe Rudy, our VP of Product and Development, and I worked together to tell the story of the challenges faced by contemporary NGS testing labs and how we’ve leveraged those challenges as opportunities to grow our suite of solutions. Here, I’d like to provide a recap of our discussion and, just maybe, ignite a spark of automation adoration in some of our readers.

Let’s start with a bird’s-eye view of the NGS testing landscape, which we discussed in some detail during our webcast. In short, the volume and variety of data available to our users is perpetually increasing. Analyzing small variants, CNVs, and structural variants in tandem is just the tip of the iceberg. Additional metrics like TMB and MSI are also becoming commonplace. Furthermore, these data can be generated in a single solution, in kits like Illumina’s TSO500, or be drawn from disparate, and sometimes redundant, systems. Lastly, NGS files and patient information are often stored in LIM systems or across complicated network configurations that need to be integrated into the input of a tertiary analysis pipeline. This presents two parallel challenges. Firstly, how does one synthesize data from various sources into a single solution? And secondly, how does one achieve this synthesis in an efficient and reproducible manner?

Before delving into the robust solutions provided by Golden Helix, Inc., we outlined the challenges faced by high-throughput NGS labs and the consequences of not meeting them head on. Profitability, the key to sustainability in NGS testing labs, comes down to efficient, well-validated pipelines. Failure to deploy a pipeline effectively and efficiently can lead to lagging profitability. While labs can’t let go of the need to have clinically validated testing standards, the pipelines that facilitate these tests run the risk of being slow, unwieldy, and inconsistent without proper automation. The automation process with VSPipeline is designed to tackle both consistency and efficiency.

The VarSeq suite is built with the needs of a wide swathe of labs in mind, and has a highly modular and configurable design. Users have fine controls over each component of the pipeline, and can pick and choose which aspects are automated and how. With the changes made in our latest release, VarSeq 2.3.0, users can create custom scripts to draw from expertly-curated sources within the AMP clinical analysis module to automatically produce comprehensive reports ready for review and sign-off. However, users still have the ability to manually inspect automatically generated projects and fine tune the results from any stage of the process.

Full-stack automation of secondary and tertiary analysis, from FASTQ to report, isn’t the only option, however. Within the clinical space, users have full latitude to design custom output scripts for common use cases like API integration or the output of machine-readable report formats. Our support team, myself included, is always excited to learn about the varied requirements of our users and assist with deploying highly specific workflows. Automation is not limited to clinical labs, either. Many researchers can benefit from the rapid and consistent application of NGS workflows to produce outputs like annotated VCFs or Excel spreadsheets for further curation and investigation.

Output isn’t the only thing that can be customized, either. As we’ve discussed, there are a variety of different data types that find themselves into NGS workflows. VarSeq’s nimble importer and malleable front-end allow for virtually unfettered scripting possibilities. Users can design robust and comprehensive scripts to define and format the input to VarSeq seamlessly with VSPipeline’s automation scripts. We provide a great deal of support to users getting started with this intimidating task, and pride ourselves in implementing workflows that can be started with a single command.

We were excited to have the opportunity to demonstrate some of these capabilities during our webcast, and I encourage anyone who would like a primer to check out the webcast and the demo portion. Unfortunately, we were told that a day-long deep dive into the varied capabilities of the VarSeq suite wasn’t compatible with the webcast format, so we encourage any interested users to reach out for more information or support regarding custom automation options.

As always, please don’t hesitate to reach out if you have any questions about our capabilities or would like to schedule a demonstration or evaluation of our software!

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