A Primer on Infectious Disease Bacterial Genomics

Tarah Lynch, Aaron Petkau, Natalie Knox, Morag Graham, Gary Van Domselaar
2016 Clinical Microbiology Reviews  
SUMMARYThe number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large
more » ... mounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.
doi:10.1128/cmr.00001-16 pmid:28590251 pmcid:PMC5010755 fatcat:7q5tsfxyzvgtrjfa6buww6pfi4