An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package.