MPRAsnakeflow’s documentation≥7.7.1-brightgreen.svg≥4.6-brightgreen.svg


MPRAsnakeflow pipeline processes sequencing data from Massively Parallel Reporter Assays (MPRAs) to create count tables for candidate sequences tested in the experiment.

MPRAsnakeflow is built on top of Snakemake. Insert your code into the respective folders, i.e. scripts, rules, and envs. Define the entry point of the workflow in the Snakefile and the main configuration in a config.yaml file.


Max Schubach (@visze) Computational Genome Biology Group Berlin Institute of Health at Charité Universitätsklinikum Berlin


If you use this workflow in a paper, don’t forget to give credits to the authors by citing the URL of the (original) repository and, if available, it’s DOI. (see above)

Installation & Getting Started

Instructions for the Installation of the program and some examples to get you started.

MPRAsnakeflow Workflows

An overview of how MPRAsnakeflow works and documentation for the MPRAsnakeflow sub workflows.

MPRAsnakeflow Examples

Muliple examples from the literature are listed for every sub workflow in MPRAsnakeflow.

Project Information

More information on the project, including the changelog, list of contributing authors, and contribution instructions.

Quick Example

To run MPRAsnakeflow, first activate the snakemake environment with the following command:

conda activate snakemake

And then run the main workflow with:

snakemake --use-conda --cores $N --configfile config/config.yaml



This utility uses mamba to efficiently query repositories and query package dependencies.


This utility sets the number of cores ($N) to be used by MPRAsnakeflow.


This file (e.g., config/config.yaml) contains the project, its objects and properties, and sub-properties and its objects that must be set before running MPRAsnakeflow.

Investigate results

After successful execution, you can create a self-contained interactive HTML report with all results via:

snakemake --report report.html --configfile conf/config.yaml

This report can be forwarded to your collaborators. An example of a generated report (using some trivial test data) can be seen here.


Feel free to leave feedback(s), ask question(s), or report bug(s) at our issues page: MPRAsnakeflow Issues.

Indices and tables