A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens

• Published in: Frontiers in Microbiology Vol. 8; p. 375
• Main Authors: Katz, Lee S., Griswold, Taylor, Williams-Newkirk, Amanda J., Wagner, Darlene, Petkau, Aaron, Sieffert, Cameron, Van Domselaar, Gary, Deng, Xiangyu, Carleton, Heather A.
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media SA 13.03.2017; Frontiers Media S.A
• Subjects: Microbiology; wgMLST; outbreak; genomic epidemiology; bacterial pathogen; foodborne; SNP pipeline

Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States ag...