Abstract
Bioinformatics tools and techniques analyzing next-generation sequencing (NGS) data are increasingly used for the diagnosis and
monitoring of infectious diseases. It is of interest to review the application of bioinformatics tools, commonly used databases and NGS
data in clinical microbiology, focusing on molecular identification, genotypic, microbiome research, antimicrobial resistance analysis
and detection of unknown disease-associated pathogens in clinical specimens. This review documents available bioinformatics
resources and databases that are used by medical microbiology scientists and physicians to control emerging infectious pathogens.