Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback v1

Maria SanchezRuth E Timme

Abstract

This protocol outlines the all the steps necessary to become a GenomeTrakr data contributor. GenomeTrakr is an international genomic reference database of mostly food and environmental isolates from foodborne pathogens. The data and analyses are housed at the National Center for Biotechnology Information (NCBI), which is a database freely available to anyone in the world. The Pathogen Detection browser at NCBI computes daily cluster results adding the newly submitted data to the existing phylogenetic clusters of closely related genomes. Contributors to this database can see how their new isolates are related to the real-time foodborne pathogen surveillance program established in the USA and a few other countries, and at the same time adding valuable new data to the reference database. ------ Although originally published as a Chapter in Methods and Protocols, Foodborne Bacterial Pathogens, the protocol has since been adapted and split into four separate protocols all of which are contained in this collection.

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