MPRAsnakeflow’s documentation

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Welcome!

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 (version ≥8.24.1 required) and is configured via a .yaml file.

Authors

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

Usage

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.

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 Turorials

Get to know MPRAsnakeflow by runnig it via jupyter notebooks or colab on small examples.

MPRAsnakeflow Examples

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

Tips & Tricks

Find our FAQ here.

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 8 environment with the following command:

conda activate snakemake

And then run the main workflow with:

snakemake --software-deployment-method conda --cores $N --configfile config/example_config.yaml

Features

Option

Description

--software-deployment-method

When conda is set, the utility uses conda to efficiently query repositories and query package dependencies. MPRAsnakeflow also can use containers via apptainer by using --software-deployment-method apptainer conda. This will use a container to run all rules but inside it will activate the pre-installed conda environments. Recommended option: --software-deployment-method apptainer conda

--cores

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

--configfile

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

Investigate results

Th ebest option to investiate your results is to have a look at the QC report.

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

snakemake --report report.html --configfile conf/example_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.

Feedback

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

Indices and tables