OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling

PeerJ

article

Ming-Hsin Tsai¹  Yen-Yi Liu²  Chih-Chieh Chen³ 

[1] Institute of Population Health Sciences, National Health Research Institutes;Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare;Institute of Medical Science and Technology, National Sun Yat-sen University;Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University

关键词: Multidimensional scaling;    Microbiome clustering;    Affinity propagation;    Disease outbreak detection;    MDS;   

DOI  :  10.7717/peerj.7600

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS.

【 授权许可】

CC BY