title: Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions.
abstract: The potential of bacterial whole-genome sequencing (WGS) to complement existing diagnostic infrastructures in clinical microbiology has been shown in proof-of-principle examples and extensively discussed. However, less attention has been drawn to bioinformatic challenges that are associated with the clinical adoption of WGS-based molecular diagnostics. This Perspective article discusses questions that are related to standard operating procedures, computational resource management, and data storage and integration in the context of recent developments in the sequencing and bioinformatics service markets.
authors.affiliation: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA.
authors.forename: W Florian
authors.initials: WF
authors.lastname: Fricke
authors.affiliation: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Rasko
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005820:Genetic Testing / Q000379:methods* / Q000639:trends; D016680:Genome, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008829:Microbiology / Q000639:trends*; D057089:Pathology, Molecular / Q000379:methods / Q000639:trends*