Genomics Pipeline V2
An enterprise-grade orchestration layer for massive-scale DNA sequencing, reducing processing time by 60% while maintaining clinical-grade reproducibility.
The Clinical Challenge
In modern oncology, speed is survival. Legacy pipelines often took 72+ hours to process a single whole-genome sequence, causing critical delays in therapeutic decision-making for late-stage patients.
Furthermore, inconsistent cloud environments led to "reproducibility drift," where the same data could yield slightly different results across different compute clusters.
Architectural Breakthrough
V2 utilizes a containerized micro-service architecture that splits sequencing data into parallelized shards. By leveraging Nextflow for workflow management and custom Kubernetes operators, we achieved deterministic scaling.
Development Journey
Conception & Benchmarking
Analyzing bottlenecks in existing GATK workflows and defining the V2 spec for sub-24h processing.
Kubernetes Integration
Migrating from static VM clusters to dynamic K8s sharding for optimized resource allocation.
Validation Trials
Benchmarking against 1,000+ public datasets to ensure zero variance in variant calling.
Full Deployment
Production release to clinical partner labs across North America and Europe.
Hybrid Storage
Intelligent tiering between S3 and FSx for Lustre to balance cost and ultra-low latency data access during high-compute phases.
CLI Dashboard
A custom Golang-based terminal interface for real-time monitoring of thousands of concurrent pipeline runs.
HIPAA Compliance
End-to-end encryption using AWS KMS and rigorous IAM policies ensuring patient data security at every pipeline stage.
Explore the Research
Full whitepaper and technical documentation available.