This workshop concluded on May 19, 2022. Workshop materials are available here.

The NCBI Pathogen Detection program provides access to bacterial pathogen genome sequence data produced by local and nationwide public health agencies. These data and the tools developed for their analysis are crucial for real-time surveillance of new outbreaks and the rapid examination of both emerging and endemic pathogens and the genes which contribute to their virulence, antimicrobial resistance and stress response. In this workshop we will show you how to mine this publicly available bacterial pathogen sequence data on the NCBI website and how to identify clinically relevant genes in your own sequences using downloadable programs such as PGAP and AMRFinderPlus.

In this workshop, you will learn how to:

• Navigate the collection of curated genomes in the NCBI Pathogen Detection system
• Download customized datasets of bacterial genomes based on isolation metadata & genomic characteristics
• Identify & access NCBI software to identify clinically relevant genes in your own bacterial sequences

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