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

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. •ClustFinder delineates clusters of microbial genomes by thresholds of genomic distances.•ClustFinder allows researchers to perform clustering analyses similar to those in public health without proprietary tools.•ClustFinder is open-source and available at github.com/Denes-Lab/ClustFinder, along with documentation and a tutorial.