KFlorek - WSLH Data Modernization

Data Modernization: Improving the usefulness of genomic data

Kelsey Florek, PhD, MPH
Senior Genomics and Data Scientist
Wisconsin State Laboratory of Hygiene
May 21, 2024

Slides live at:
www.k-florek.net/talks

Supported By

AWS Diagnostic Development Initiative (DDI)

Necessities of Next Generation Sequencing Capacity Building
Blueprints for an NGS Data Solution
Simplifying Genomics for Public Health Partners

Expanding Genomic Sequencing Capacity

Pre SARS-CoV-2 Pandemic

4x Illumina MiSeq
1x ONT MinION

Post SARS-CoV-2 Pandemic

4x Illumina MiSeq
2x NextSeq 2000
1x ONT GridION
1x Eppendorf epMotion
1x Tecan Fluent 780 NGS Dream Prep

Over 900% increase in sequencing data generation capacity

NGS Data Storage

Improvements in Analytical Approaches

Old Approach

Entirely Python Based
Limited logging and fault tolerance
Required installing complicated and often conflicting dependencies

New Approach

Nextflow - Nf-Core Based
Containerized Steps
Detailed Logging
Compatible with a variety of Cloud and HPC environments
Supports a high degree of job parallelization and horizontal scalability

~~Necessities of Next Generation Sequencing Capacity Building~~
Blueprints for an NGS Data Solution
Simplifying Genomics for Public Health Partners

Bioinformatics analytical infrastructure

Highly scalable and capable of managing burst data
Highly reliable and fault tolerant
Cost effective
Adaptable to changing needs
Detailed logging and traceability

WSLH Bioinformatics Analytical Infrastructure

AWS Batch

AWS Batch automatically provisions compute resources and optimizes the workload distribution based on the quantity and scale of the workloads.

AWS Batch

Nextflow Tower is an intuitive centralized command post that enables data analysis at scale. With Tower, users can easily launch, manage, and monitor scalable Nextflow data analysis pipelines and compute environments on-premises or across the cloud providers of their choice.

Seqera Labs - Nextflow Tower