Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods
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- 作者：Johanne Ahrenfeldt ; Carina Skaarup ; Henrik Hasman ; Anders Gorm Pedersen…
- 关键词：Phylogeny ; Evolution ; Benchmark ; WGS
- 刊名：BMC Genomics
- 出版年：2017
- 出版时间：December 2017
- 年：2017
- 卷：18
- 期：1
- 全文大小：1357KB
- 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
- 出版者：BioMed Central
- ISSN：1471-2164
- 卷排序：18
文摘
BackgroundWhole 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.