id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-003316-r5te5xob	Balloux, Francois	From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic	2018-12-17		.txt	text/plain	7340	327	34	WGS-based strain identification gives a far superior resolution In principle, WGS can provide highly relevant information for clinical microbiology in near-real-time, from phenotype testing to tracking outbreaks. As an example, genome assembly might appear to be a bottleneck for real-time WGS diagnostics, but is probably rarely required; sufficient characterization of an isolate can be made by analysis of the k-mers in the raw sequence data, which is orders of magnitude faster. These include, among others: the current costs of WGS, which remain far from negligible despite a common belief that sequencing costs have plummeted; a lack of training in, and possible cultural resistance to, bioinformatics among clinical microbiologists; a lack of the necessary computational infrastructure in most hospitals; the inadequacy of existing reference microbial genomics databases necessary for reliable AMR and virulence profiling; and the difficulty of setting up effective, standardized, and accredited bioinformatics protocols.	./cache/cord-003316-r5te5xob.txt	./txt/cord-003316-r5te5xob.txt