Episode 129: Genomics on the Frontier: Bactopia, Bioinformatics, and Pathogen Surveillance with Robert Petit

Host Andrew Page is joined by Robert Petit from the Wyoming Public Health Laboratory. Robert, a key developer of the Bactopia pipeline, shares insights into how this end-to-end tool is transforming bacterial genomic surveillance.

They dive into the origins of Bactopia, its applications in public health, and Robert's experience leading genomic projects in a rural setting. Discover how Bactopia streamlines pathogen detection, improves documentation, and integrates with other tools to deliver fast and accurate results. Listen in as they discuss new innovations in bioinformatics, including visualizations and human-read filtering, and explore future projects like CamelHUMP, designed to simplify sequence-based typing. Recorded live at the Microbial Bioinformatics Hackathon in Bethesda, Maryland, this episode brings you the latest in pathogen genomics and the challenges and rewards of working on the frontier of public health.

Key Points

1. Bactopia Pipeline Development

• Originated from Staphopia project analyzing Staphylococcus genomes
• Provides rapid, comprehensive bacterial genome analysis
• Supports multiple pathogen detection with flexible processing

2. Emerging Bioinformatics Tools

• Developing CamelHUMP for simplified sequence-based typing
• Implementing human read scrubbing with multiple filtering options
• Received Chan Zuckerberg Initiative grant for visualization improvements

3. Public Health Genomics in Rural Settings

• Wyoming Public Health Laboratory conducts extensive genomic surveillance
• Collaborates internationally (e.g., with Oman Central Public Health Laboratory)
• Addresses unique challenges of frontier state public health

Take-Home Messages

• Open-source tools can dramatically simplify complex genomic analysis
• Flexibility and documentation are critical in bioinformatics software development
• Rural public health labs are at the forefront of genomic innovations