ClustFinder: A tool for threshold-delineated clustering of microbial isolates by pairwise genomic distance

Harleen K Chaggar; Lauren K Hudson; Ryan Kuster; Katie N Garman; John R Dunn; Thomas G Denes

doi:10.1016/j.mimet.2023.106788

ClustFinder: A tool for threshold-delineated clustering of microbial isolates by pairwise genomic distance

J Microbiol Methods. 2023 Aug:211:106788. doi: 10.1016/j.mimet.2023.106788. Epub 2023 Jul 17.

Authors

Harleen K Chaggar¹, Lauren K Hudson¹, Ryan Kuster², Katie N Garman³, John R Dunn³, Thomas G Denes⁴

Affiliations

¹ Department of Food Science, University of Tennessee, Knoxville, TN, USA.
² Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.
³ Tennessee Department of Health, Nashville, TN 37243, USA.
⁴ Department of Food Science, University of Tennessee, Knoxville, TN, USA. Electronic address: tdenes@utk.edu.

PMID: 37468111
DOI: 10.1016/j.mimet.2023.106788

Abstract

This paper presents ClustFinder, a command line tool designed to automate clustering of genomes based on genomic distance. This tool will aid researchers and public health professionals in the identification of epidemiological clusters. Here, we demonstrate the usage of ClustFinder with example datasets. ClustFinder is available at github.com/Denes-Lab/ClustFinder.

Keywords: Bioinformatics; Genomics; Outbreak detection; Tool.

Publication types

Research Support, U.S. Gov't, P.H.S.

MeSH terms

Cluster Analysis
Genome
Genomics*
Software*