README.md

In openPrimeR: Multiplex PCR Primer Design and Analysis

openPrimeR

Synopsis

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 setes 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. The R package includes a Shiny application that provides a comprehensive and intuitive user interface for the core functionalites of the package.

More information

There is a Conda repository for openPrimeR available. For more information on how to install the third-party dependencies for openPrimeR, we refer to the corresponding user-space repository, which provides installation routines.

Docker Instructions

Our docker image is available at dockerhub. In order to use the docker image, you need to install docker on your system and activate the docker daemon.

After logging in with your docker account, in a console, enter

docker pull mdoering88/openprimer

to retrieve the latest docker image of the tool. Since the image is quite large the download (~4 GB) may take some time, especially if your internet connection is not very fast.

To run the image, enter

docker run -p 3838:3838 --rm mdoering88/openprimer

After this, the tool is available by accessing localhost:3838 in your web browser.

In case you want to have more control of the image you are running or you want to study the output of the tool, you can execute

docker run --rm -p 3838:3838 -v /tmp/logs/:/var/log/shiny-server/ mdoering88/openprimer:latest

With this call, the tool's log file is stored in the /tmp/logs/ folder on your system with a filename starting with shiny-shiny). During the session, you can use

tail -f shiny-shiny-X.txt

to retrieve the current status messages.

Moreover, in the above call to Docker, we have specified a tag, namely :latest, which means that we have started the most recent version of the tool. In case that no tag is provided, the latest available Docker image is used.

You can also work with the openPrimeR API through the container by executing

docker run -rm -it mdoering88/openprimer bash

and then starting an R session and loading the openPrimeR package.

Changelog

Take a look at the CHANGELOG to view recent changes to the project.

openPrimeR documentation built on Nov. 16, 2020, 2 a.m.