Scaling Genomic Sequencing Capacity by 10-fold at the Wisconsin State Laboratory of Hygiene
Read the full case studyAim
Rapidly adapt internal processes to handle growing volumes of complex sequencing data to enable efficient data analysis at scale.Challenges
- →Limited scalability and efficiency in handling largescale genomic data.
- →Difficulty building standardized workflows accessible to partner laboratories.
- →Impractical, labor-intensive parallel processing and fault tolerance with existing frameworks.
Solution
Nextflow
parallelization, fault tolerance and logging
nf core
peer-reviewed, standardized pipelines
Seqera
workflow optimization at scale
Results
Prior to the COVID-19 pandemic, WSLH were processing 50-100 sequencing samples per week totaling to less than a terabyte of genomic data a year. By utilizing Seqera platform and Nextflow, WSLH was able to dynamically scale this capacity by 10-fold and now processes over 10 terabytes of pathogen genomic data a year with minimal alterations to their AWS Batch environments. This has enabled the continued expansion into sequencing new bacterial, viral, and eukaryotic pathogens. Such scalable cloud solutions also provided robust data storage and querying capabilities for easy data access.
10x
Opportunity
Real-time disease monitoring
Create publicly accessible, real-time dashboards for monitoring infectious disease epidemiology.
Expanded pathogen capacity
Capacity to expand scope of pathogens that can be sequenced, to augment public health response.
Cross-organizational standardization
Standardize genomic workflows across organizations to foster collaboration and sharing of public health data.
About
The Wisconsin State Laboratory of Hygiene (WSLH) is the state’s public, environmental and occupational health laboratory. As part of the University of Wisconsin-Madison and as an auxiliary unit reporting to the University of Wisconsin School of Medicine and Public Health, the WSLH is committed to exploring new ideas which benefit the state, the nation and the world. Through analytical services, research and development, public health programs, laboratory proficiency testing, and training and education of students and professionals, the WSLH’s work is vital to Wisconsin’s and the nation’s public and environmental health.
To learn more, visit https://www.slh.wisc.edu/