Genomic sequencing impacts every one of the 8 billion people who share this planet.
At the individual or human level, its widening availability improves a diagnosis and helps understand our disease risk.
On a global perspective, animal and plant genomics are key to preserving our diverse environment and to feeding our growing population through times of drought and disease.
The utilization and demand for large-scale genomics continues to grow rapidly and reductions in the cost of sequencing have enabled research and analysis to scale higher.
Gencove is a leader in the field of genomic data generation, analysis, and management. Its vision is for the application of ubiquitous sequencing to enable a healthier and more sustainable civilization. Gencove’s customers are true demonstrators of the diverse areas of impact from genomics. It is from utilizing low-pass whole genome sequencing to identify and predict congestive heart failure in cattle to working with a top pharmaceutical company to develop novel approaches to imputation, unlocking new insights on structural variation from existing short-read sequencing datasets.
Behind every application of genomics is a series of compute-intensive stages of data preparation and analysis. Sentieon’s team of computer scientists develop award winning implementations of these key genomics analysis stages and accelerate these compute-intensive parts of the pipeline, reducing the time and cost by over 5x. Sentieon’s customers have processed almost 3 Exabytes of genomic data to date.
With the most efficient software implementation in hand, the next question for Sentieon was how to reduce the cost still further for clients like Gencove.
“We saw an opportunity to further reduce computing costs and energy demands for genomic applications using Arm CPUs after they became more widely available in the cloud and decided to port our suite to Arm.”- Don Freed, Senior Bioinformatics Scientist at Sentieon.
AWS Graviton is a family of Arm architecture processors that are developed by AWS using Arm Neoverse core and system IP. The processors offer the best price-performance across a wide range of workloads, with a variety of instance types optimized for general purpose, compute, memory or storage heavy workloads.
Sentieon and Gencove discovered that using AWS Graviton3 would substantially reduce costs.
Figure 1. Cost of Whole Genome Sequencing across AWS EC2-based instances.
To demonstrate potential cost savings, Arm has benchmarked the publicly available HG002 Illumina short-read 30x WGS (Whole Genome Sequencing) data set, using Sentieon DNAscope to align and call variants using the hg38 reference, on a variety of AWS instances types.
With the publicly available 30x WGS (Whole Genome Sequencing) HG002 Illumina short-read data set, aligning against the hg38 reference genome using Sentieon software against a variety of AWS’s compute-optimized instance types, the cost benefits of AWS Graviton3-based instances can be demonstrated.
In every case tested, AWS Graviton3-based c7g instances yielded at least a 35% reduction in cost compared to all other available AWS compute-optimized x86-based AWS EC2 instance types.
Gencove co-founder and CTO, Tomaz Berisa remarked, “Gencove is confident it has some of the world’s lowest compute costs for these types of analyses. We only achieve this by combining Sentieon with Arm servers on AWS”
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