Abstract

The arrival of next-generation sequencing (NGS) has changed the field of microbial genomics research. In comparison to traditional automated Sanger capillary sequencing, NGS allows for a more comprehensive analysis of microbial genetic and genomic variants at a lower cost. NGS technologies have expanded the versatility of standard typing approaches (MLST, MLVA, rMLST, and cgMLST) from assessing nucleotide variation in hundreds of DNA sequences for a few genes, to new typing methods (WGS, NGMLST, and HiMLST) that can screen thousands of amplicons and full genomes. Indeed, the large amount of data produced by NGS required the development of advanced analytic and statistical methods and frameworks. Here, we describe standard and new approaches for microbial sequence typing at gene and genome levels, including guidelines for choosing analytical pipelines and methods, and computational frameworks. We also present several applications of these approaches to disciplines such as genotyping, phylogenetics and phylogenomics, and molecular epidemiology.