BackgroundCluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration.ResultsGraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings.ConclusionsGraphSNP is freely available athttps://github.com/nalarbp/graphsnp. An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use athttps://graphsnp.fordelab.com.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12859-023-05332-x.