Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.

ABSTRACT:

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 benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods.

Results

Our aim was to create a benchmark data set that mimics sequencing data of the sort that might be collected during an outbreak of an infectious disease. This was achieved by letting an E. coli hypermutator s

SUBMITTER: Ahrenfeldt J 

PROVIDER: S-EPMC5217230 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature