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GenomeTrakr Network

The Geno​​meTrakr Network helps quickly identify genetic sources of foodborne outbreaks. By connecting public health and university laboratories that utilize whole genome sequencing (WGS) for pathogen identification, GenomeTrakr allows these laboratories to share genomic and geographic data from foodborne outbreaks as they occur.

Visit FDA’s GenomeTrakr Site
Questions?

Contact the Food Safety team: [email protected]

About GenomeTrakr

GenomeTrakr labs perform whole genome sequencing bacteria isolates, as well as parasites and viruses. Food and environmental samples are sequenced and uploaded to the GenomeTrakr database by federal (e.g., FDA, USDA, CDC, NOAA), state, academic and international partners. Laboratories that participate in the GenomeTrakr Network use the data to identify foodborne outbreaks and contaminated products.

maps of GenomeTrkr labs in the US and outside the US

Domestic and international laboratories that participate in the GenomeTrakr network. (Source: FDA)

Data Curation and Bioinformatic Analyses

GenomeTrakr Network Data

The data, which are housed in public databases at the National Center for Biotechnology Information (NCBI), can be accessed by researchers and public health officials for real-time comparison and analysis that can speed foodborne illness outbreak investigations and reduce foodborne illnesses and death

WGS Software and Platform Training

FDA CFSAN has developed short training modules to help laboratories utilize various tools and platforms when analyzing WGS data. These videos can also be found on the  Galaxy Trakr's YouTube channel. 

Galaxy Trakr Overview

Galaxy Trakr is an open source, web-based platform for accessible, reproducible and transparent computational biomedical research. Laboratories that participate in the GenomeTrakr Network upload their whole genome sequencing data to the web-based platform to perform quality assessments of sequencing data, identify links between clinical isolates and positive food/environmental samples, including those at the National Center for Biotechnology Information sequence read archive and explore new methodologies such as metagenomics. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows.

Learn more about Galaxy Trakr

GALAXYTRAKR INTERFACE

This tutorial walks the viewer through the four parts of the Galaxy Trakr interface: the tool list on the left, the viewing panel in the middle and the analysis and data history on the right.

SEQSERO TRAINING

This training video demonstrates how users can utilize Seqsero software to determine serotypes, or groups within a single species of microorganisms, such as bacteria or viruses, which share distinctive surface structures.

LEARN MORE

Additional Resources

Training Resources

GenomeTrakr:

GenomeTrakr Resources

  • Sample Transfer Template
    Document
    Many laboratories are looking to outside entities to source isolates for sequencing. The FDA has provided this template for the transferring materials from outside sources to the laboratory. This template can be customized to fit your laboratory's needs.
  • APHL/FDA Bioinformatics Training
    Online Course; login required
    APHL and FDA have partnered to create a one-hour bioinformatics webinar focused on the basics of phylogeny and how it can be applied to whole genome sequencing data during outbreak investigations.