Abstract Summary Optical mapping is a molecular technique capturing specific patterns of fluorescent labels along DNA molecules. It has been widely applied in assisted-scaffolding in sequence assemblies, microbial strain typing and detection of structural variations. Various computational methods have been developed to analyze optical mapping data. However, existing tools for processing and visualizing optical map data still have many shortcomings. Here, we present OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses. Availability and implementation OMTools is implemented in Java 1.8 and released under a GPL license. OMTools can be downloaded from https://github.com/aldenleung/OMTools and run on any standard desktop computer equipped with a Java virtual machine. Supplementary information Supplementary data are available at Bioinformatics online.