Containerization: the silent hero of the COVID-19 variant surveillance effort.

Kelsey Florek, PhD, MPH
Senior Genomics and Data Scientist
Wisconsin State Laboratory of Hygiene
December 9, 2021

Slides live at:



Barriers to Bioinformatics in Public Health Laboratories

  • vast landscape of compute infrastructure
    • on-premise servers/workstations
    • high performance compute cluster
    • public cloud
    • none
  • limited experience working with open source software
  • limited informatics support beyond desktop/network

What is StaPH-B?

  • State Public Health Bioinformatics
  • provide training and resources for applied bioinformatics
  • support construction and maintenance of bioinformatics infrastructure in state Public Health laboratories
  • partner with Centers for Disease Control and Prevention and the Association of Public Health Laboratories


Curtis Kapsak


  • Dockerfiles >90 different open source bioinformatic analysis tools
  • Data QC
  • Genome Assembly
  • Annotation
  • Classification

SARS-CoV-2 Variant Surveillance


Dr. Erin Young


Titan Illumina PE
Kevin Libuit
Dr. Robert Petit III
Frank Ambrosio

Keeping up with SARS-CoV-2 Evolution

2 mutations per month in the 29,903 base genome



The Takeaways

  • Containerization solves many problems in Bioinformatics
    • Distribution of open source software
    • Repeatability
    • Simplifying development of workflows
  • Infectious disease surveillance and research is built on open source
  • Containerization has been instrumental throughout this pandemic allowing a wide range of laboratories to contribute global surveillance effort


  • Special Thanks
    • Eva Bojorges
    • AurĂ©lien Suarez