crossmark A Primer on Infectious Disease Bacterial Genomics Tarah Lynch,a,b Aaron Petkau,c Natalie Knox,c Morag Graham,c,d Gary Van Domselaarc,d Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canadaa; Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canadab; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canadac; Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canadad SUMMARY ..................................................................................................................................................882 INTRODUCTION ............................................................................................................................................882 PREPARATION ..............................................................................................................................................882 Project Management .....................................................................................................................................883 Experimental Design .....................................................................................................................................883 Computational infrastructure resources ...............................................................................................................884 (i) Estimating computational resources .............................................................................................................885 (ii) Data storage requirements ......................................................................................................................885 (iii) Cloud-based computing ........................................................................................................................885 Software and workflow management .................................................................................................................886 (i) Data analysis reproducibility......................................................................................................................887 Laboratory resources: choosing an HTS platform......................................................................................................888 (i) Read length.......................................................................................................................................888 (ii) Read type ........................................................................................................................................888 (iii) Error types and rates.............................................................................................................................888 (iv) Coverage ........................................................................................................................................889 SAMPLE PROCESSING AND DATA GENERATION ..........................................................................................................889 DNA Extraction and Template Assessment...............................................................................................................889 HTS Library Preparation and Sequencing.................................................................................................................889 PRIMARY ANALYSIS ........................................................................................................................................889 SECONDARY ANALYSIS ....................................................................................................................................890 Reference Mapping and Variant Calling ..................................................................................................................890 Reference mapping issues.............................................................................................................................891 Selecting a reference genome.........................................................................................................................892 Quality control of input data...........................................................................................................................892 Generating a read pileup ..............................................................................................................................892 Quality control of a read alignment pileup ............................................................................................................892 Variant calling, filtering, and annotation ...............................................................................................................892 De Novo Assembly........................................................................................................................................893 Choosing de novo assembly software..................................................................................................................893 Evaluating de novo assemblies.........................................................................................................................893 TERTIARY ANALYSIS ........................................................................................................................................893 Bacterial Genome Annotation............................................................................................................................893 Recombination and Mobile Elements ....................................................................................................................896 Recombination ........................................................................................................................................896 Mobile genetic elements ..............................................................................................................................896 (i) Transposons ......................................................................................................................................896 (ii) Plasmids..........................................................................................................................................897 (iii) Prophage ........................................................................................................................................897 Phylogenetics to Phylogenomics.........................................................................................................................897 General phylogenetic concepts .......................................................................................................................897 Inferring phylogenetic trees ...........................................................................................................................898 Phylogenomics ........................................................................................................................................898 (i) Alignment-based phylogenies ...................................................................................................................899 (ii) Alignment-free phylogenies .....................................................................................................................900 (iii) Gene-by-gene phylogenies .....................................................................................................................901 (iv) Choosing a method for phylogeny generation. .................................................................................................901 (continued) Published 24 August 2016 Citation Lynch T, Petkau A, Knox N, Graham M, Van Domselaar G. 2016. A primer on infectious disease bacterial genomics. Clin Microbiol Rev 29:881–913. doi:10.1128/CMR.00001-16. Address correspondence to Tarah Lynch, [email protected]. Copyright © 2016, American Society for Microbiology. All Rights Reserved. October 2016 Volume 29 Number 4 Clinical Microbiology Reviews cmr.asm.org 881 Lynch et al. HTS IN THE CONTEXT OF SPECIFIC APPLICATIONS........................................................................................................901 Bacterial Typing ..........................................................................................................................................902 Molecular Epidemiology .................................................................................................................................902 Bacterial Pathogenomics .................................................................................................................................903 GLOBAL ACCESSIBILITY OF GENOMICS DATA.............................................................................................................904 CONCLUSIONS .............................................................................................................................................904 APPENDIX ..................................................................................................................................................904 Glossary ..................................................................................................................................................904 REFERENCES ................................................................................................................................................905