openPrimeR is an R package providing methods for designing, evaluating, and comparing primer sets for multiplex polymerase chain reaction (PCR). The package provides a primer design function that generates novel primer sets by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers.

Moreover, existing primer sets can be evaluated according to their coverage and their fulfillment of constraints on the PCR-relevant physicochemical properties. For PCR tasks for which multiple possible primer sets exist, openPrimeR can facilitate the selection of the most suitable set by performing comparative analyses.

There are two openPrimeR package. openPrimeR provides a backend providing all relevant functionalities, while openPrimeRui entails the Shiny application that provides a user interface to the package.

If you have suggestions for improving openPrimeR or if you run into technical problems, please contact with a detailed description of your feedback.


2017-09-29: openPrimeR is now available via Bioconductor.

2017-08-21: openPrimeR version 0.99.0 is publicly available via GitHub.


If you are interested in using the openPrimeR R package, the simplest installation route is via Bioconductor. The corresponding frontend is available via the openPrimeRui package. The development version of both openPrimeR and openPrimeRui is available through GitHub .

If you are only interested in employing the openPrimeR frontend, you can simply use our Docker container, which contains all dependencies for using the tool.