Article
Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.
BMC genomics - 5 Jan 2017
Ahrenfeldt Johanne, Skaarup Carina, Hasman Henrik, Pedersen Anders Gorm, Aarestrup Frank Møller, Lund Ole
Abstract excerpt
BACKGROUND: Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of...
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