Workshop 3 - Whole Genome and Metagenomic Sequence Analyses: A Tutorial and Hands-on Workshop to Help Understand This Process

Friday, July 12 and Saturday, July 13, 2024 (8:30 a.m. - 5:00 p.m.)

Workshop Registration Fees

  • Members $820.00
  • Non-Members $920.00
  • Late-fee $75.00

Register Now

 Late Rate Effective June 18, 2024.

Workshop rates are available for IAFP students upon request. 

IAFP Workshop Cancellation Policy:  Registration fees, less a $100 administration fee and any
applicable bank charges, will be refunded for written cancellations received by June 27, 2024.  No
refunds will be made after June 27, however, the registration may be transferred to a colleague
who is NOT currently registered with written notification.  Registrations cannot be carried to any
future meetings.

Photo Policy:  We occasionally use photographs of attendees in our promotional material.  By
attending, you agree to such usage.

Other:  Any modifications to payment method will incur a $25 processing fee.

Refunds will be processed when received.

Workshop Description

From genome sequences to databases to analysis methods and software, the amount of sequence data available for food safety continues to grow. More data can add precision and enable faster and more efficient decision-making in the preparedness, response, and prevention of foodborne outbreaks by improving our understanding of important questions surrounding pathogenicity, microbiological risk assessments, traceability and more. Whole genome and metagenomic sequencing is being used globally to track outbreak strains of bacteria, monitor microbial communities and understand changes in populations of organisms based on temporal and forced stimuli. These technologies are more complex than past methodologies and have more components that need to be understood. What is NGS, WGS and metagenomic or Quasi-metagenomic? What kind of different sequencers are available, and which one should I choose for my studies? How do I analyze my data and what kind of quality control tools exist for sequence data? How do I assemble short-read, long-read or a metagenomic data set? What does the data mean? And how is FDA and CDC using the data? This expanded two-day workshop seeks to shed light on these questions so that the student will have ample time to gain a more holistic view of the applications of next generation sequencing. We will provide sessions on technology, data analysis and data interpretation that the FDA, CORE, Compliance and CDC, employ for outbreak investigations and regulatory decision-making. Each attendee will be analyzing whole genome sequencing and metagenomic datasets to perform quality control, assembly, build phylogenetic trees, identify genes of interest (such as AMR, virulence and stress response genes) and visualize the data utilizing open-source tools such as GalaxyTrakr, and Pathogen Detection Website. Upon return from the workshop the knowledge gained, and the tools learned can be implemented for whole genome and metagenomic sequencing data analysis in your lab.

Who Should Attend

Government, Industry, University

Workshop Instructors

  • Laura Gieraltowski, CDC, Atlanta, GA, USA
  • Maria Hoffmann, U.S. Food and Drug Administration, College Park, MD, USA
  • Katheryn Judy, U.S. Food and Drug Administration, College Park, MD, USA
  • Arjun Prasad, NCBI, Bethesda, MD, USA
  • Padmini Ramachandran, U.S. Food and Drug Administration – CFSAN, College Park, MD, USA
  • Daniela Schoelen, U.S. Food and Drug Administration, College Park, MD, USA
  • Charles Strittmatter, U.S. Food and Drug Administration – CFSAN, College Park, MD, USA
  • Victoria Wagoner, U.S. Food and Drug Administration, College Park, MD, USA

Workshop Organizers

  • Maria Hoffmann, US FDA, College Park, MD, USA
  • Padmini Ramachandran, U.S. Food and Drug Administration – CFSAN, College Park, MD, USA