Hosted at Bioinformatics, Leipzig University, Germany.

# Homepage of BarMap-QA

BarMap-QA – cotranscriptional folding simulations of RNA molecules with quality assurance.

## Description

BarMap-QA is a pipeline enabling the user to easily conduct cotranscriptional folding analyses of a given RNA sequence and to assess the quality of the generated data. It builds on the latest version of the more general BarMap framework and adds a lot of helpful scripts and programs around it that generate the required input, perform pre- and post-processing tasks, evaluate the simulation quality, and finally plot the results. The publication accompanying this distribution contains a comprehensive step-by-step tutorial to help you getting started with our analysis work flow.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

A copy of the GNU General Public License can be obtained from the official GNU GPLv3 website.

## Docker image

BarMap-QA is available as a portable, easy-to-use Docker image that runs on all major platforms and has no requirements but a standard installation of the Docker Community Edition and at least 8 GB of main memory. It is hosted on Docker Hub and can be obtained by simply running docker pull xilef1337/barmap-qa on the command line.

To download and update the image and run the container, we provide this wrapper script for Linux. On Windows and macOS, open a PowerShell or a terminal (respectively) and run docker run --rm -v C:\path\to\my\directory:/host -it xilef1337/barmap-qa, where C:\path\to\my\directory is the working directory that is mounted inside the /host directory of the container. All output files will be written there.

## Source distribution

Here you can download the latest version of the BarMap-QA as a source distribution for Linux. However, we recommend to use the provided Docker image (see above), which is already properly set up and requires no external dependencies. If you choose to perform a manual installation, please extract the downloaded archive and follow the steps in the file README.md.

## Citation

If you use this software for your research, please cite the following publication:

Felix Kühnl, Peter F. Stadler, Sven Findeiß
"Assessing the Quality of Cotranscriptional Folding Simulations"
Sept 2019, submitted to Springer Nature.

A preprint of this publication is available on bioRxiv.

## Contact

Should you have any questions, suggestions, or bug reports, do not hesitate to write us an email.

Corresponding author: Sven Findeiß, sven@bioinf.uni-leipzig.de

Bioinformatics, Leipzig University, Germany.