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Clin Microbiol Rev. 2016 Oct;29(4):881-913. doi: 10.1128/CMR.00001-16. Epub 2016 Sep 7.

A Primer on Infectious Disease Bacterial Genomics.

Author information

1
Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada tarah.lynch@ahs.ca.
2
Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.
3
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
4
Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.

Abstract

The 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 amounts 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.

PMID:
28590251
PMCID:
PMC5010755
DOI:
10.1128/CMR.00001-16
[Indexed for MEDLINE]
Free PMC Article

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