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Accelerating bioinformatics implementation in public health.

Kevin G Libuit1, Emma L Doughty1, James R Otieno1

  • 1Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA.

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Summary
This summary is machine-generated.

An open bioinformatics ecosystem using Terra and Theiagen workflows addresses public health laboratory needs for standardized, reproducible genomic analyses. This scalable solution supports genomic epidemiology and has been used for over 5 million sample analyses globally.

Keywords:
Terrabioinformaticsepidemiologygenomepublic healthsequencing

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Area of Science:

  • Bioinformatics
  • Genomic Epidemiology
  • Public Health Laboratory Science

Background:

  • Implementing bioinformatics in public health laboratories (PHLs) faces challenges in standardization, reproducibility, and scalability.
  • PHLs require secure, portable, and auditable data analysis solutions that fit operational constraints.
  • Existing bioinformatics tools may not meet the specific needs of public health practitioners.

Purpose of the Study:

  • To establish an open bioinformatics ecosystem tailored for public health laboratories.
  • To provide standardized, user-friendly bioinformatics workflows for genomic analysis.
  • To enhance genomic epidemiology capabilities within PHLs.

Main Methods:

  • Utilized Terra, a web-based platform with a graphical user interface, for accessible bioinformatics analysis.
  • Developed Theiagen workflows for genome assembly, quality control, characterization, and phylogenetic analysis.
  • Employed open-source, containerized software and WDL for standardization and interoperability, with code available on Dockstore and GitHub.

Main Results:

  • Theiagen workflows generate standardized outputs for downstream analysis and visualization.
  • The ecosystem has been adopted by over 90 PHLs in 40+ countries.
  • Over 5 million sample analyses have been performed using these workflows in the past two years.

Conclusions:

  • The developed open bioinformatics ecosystem effectively meets the requirements for bioinformatics implementation in PHLs.
  • The Terra platform and Theiagen workflows provide a scalable, reproducible, and auditable solution for genomic epidemiology.
  • Continued development and adoption of this ecosystem will further benefit public health laboratories worldwide.