Reducing costs by 50% while processing population-scale genomics with Mountpoint for Amazon S3 and AWS Batch

This article describes how Oxford Nanopore Technologies built EPI2ME Cloud, a genomics analysis platform using AWS services to process population-scale human genomes with 50% cost reduction.

• Mountpoint for Amazon S3 eliminates data staging bottleneck by mounting S3 as local filesystem
• AWS Batch orchestrates containerized jobs with automatic scaling for hundreds of parallel genomes
• Nextflow DSL2 pipeline (wf-human-variation) performs variant calling on long-read sequencing data
• Amazon EC2 Spot instances provide cost-optimized compute resources for horizontal scaling
• Architecture processes 1,400 tasks per genome, pulling only required 500MB instead of full 200GB
• Data encrypted at rest/transit with IAM controls and AWS PrivateLink for security compliance
• System achieves hundreds of genomes weekly with minimal manual oversight and full auditability

Oxford Nanopore's cloud platform demonstrates how combining AWS services enables secure, scalable, cost-efficient genomics analysis for precision medicine initiatives.