.. _Homepage: ==================================== MPRAsnakeflow's Documentation ==================================== .. image:: https://img.shields.io/badge/GitHub-repository-brightgreen?logo=github :alt: GitHub Repository :target: https://github.com/kircherlab/MPRAsnakeflow .. image:: https://img.shields.io/github/v/release/kircherlab/MPRAsnakeflow :alt: Latest Release :target: https://github.com/kircherlab/MPRAsnakeflow/releases/latest .. image:: https://zenodo.org/badge/347005871.svg :alt: DOI :target: https://doi.org/10.5281/zenodo.18163777 .. image:: https://img.shields.io/github/license/kircherlab/MPRAsnakeflow :alt: License :target: https://github.com/kircherlab/MPRAsnakeflow/blob/master/LICENSE .. image:: https://img.shields.io/badge/snakemake-≥8.24.1-brightgreen.svg :alt: Snakemake :target: https://snakemake.github.io/ .. image:: https://img.shields.io/badge/conda->24.7.1-brightgreen.svg :alt: Conda :target: https://github.com/conda-forge/miniforge .. image:: https://github.com/kircherlab/MPRAsnakeflow/actions/workflows/main.yml/badge.svg :alt: Tests :target: https://github.com/kircherlab/MPRAsnakeflow/actions/workflows/main.yml .. image:: https://img.shields.io/github/issues/kircherlab/MPRAsnakeflow :alt: GitHub Issues :target: https://github.com/kircherlab/MPRAsnakeflow/issues .. image:: https://img.shields.io/github/issues-pr/kircherlab/MPRAsnakeflow :alt: GitHub Pull Requests :target: https://github.com/kircherlab/MPRAsnakeflow/pulls **Welcome!** MPRAsnakeflow is a pipeline designed to process 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 Citation --------- If you use MPRAsnakeflow in your work, please cite our recent preprint: .. epigraph:: **Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow** Jonathan D. Rosen, Arjun Devadas Vasanthakumari, Kilian Salomon, Nikola de Lange, Pyaree Mohan Dash, Pia Keukeleire, Ali Hassan, Alejandro Barrera, Beniamin Krupkin, Grace Oualline, Martin Kircher, Michael I. Love, Max Schubach *Genome Research* (2025). `10.1101/gr.281462.125 `_ Usage ----- If you use this workflow in a paper, don't forget to give credit to the authors by citing the URL of the (original) repository. Installation & Getting Started ------------------------------ Instructions for installing the program and examples to help you get started. MPRAsnakeflow Workflows ----------------------- An overview of how MPRAsnakeflow works and documentation for the MPRAsnakeflow sub-workflows. MPRAsnakeflow Tutorials ----------------------- Get to know MPRAsnakeflow by running it via Jupyter notebooks or Google 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 environment with the following command: .. code-block:: bash conda activate snakemake Then run the main workflow with: .. code-block:: bash snakemake --software-deployment-method conda --cores $N --configfile config/example_config.yaml -------- Features -------- .. list-table:: :widths: 25 80 :header-rows: 1 * - Option - Description * - ``--software-deployment-method`` - When ``conda`` is set, the utility uses conda to efficiently query repositories and manage package dependencies. MPRAsnakeflow can also use containers via Apptainer by using ``--software-deployment-method apptainer conda``. This will use a container to run all rules but will activate the pre-installed conda environments inside it. Recommended option: ``--software-deployment-method apptainer conda``. * - ``--cores`` - This utility sets the number of cores (``$N``) to be used by MPRAsnakeflow. * - ``--configfile`` - This file (e.g., ``config/example_config.yaml``) contains the project configuration, including objects and properties that **must** be set before running MPRAsnakeflow. ------------------- Investigate Results ------------------- The best option to investigate your results is to review the QC report. (In development) After successful execution, you can create a self-contained interactive HTML report with all results via: .. code-block:: bash snakemake --report report.html --configfile config/example_config.yaml This report can be shared with collaborators. An example of a generated report (using some trivial test data) can be seen `here `_. -------- Feedback -------- Feel free to leave feedback, ask questions, or report bugs on our issues page: `MPRAsnakeflow Issues `_. Indices and Tables ================== * :ref:`genindex` * :ref:`search` .. toctree:: :caption: Installation & Getting Started :name: getting-started :maxdepth: 1 :hidden: 1_getting_started/quickstart 1_getting_started/install 1_getting_started/config 1_getting_started/cluster .. toctree:: :caption: Workflows :name: mprasnakeflow-workflows :maxdepth: 1 :hidden: 2_workflows/overview 2_workflows/assignment 2_workflows/experiment .. toctree:: :caption: Further documentation :name: mprasnakeflow-further-documentation :maxdepth: 1 :hidden: 3_further_documentation/best_practice 3_further_documentation/tutorial 3_further_documentation/adapter .. toctree:: :caption: Examples :name: mprasnakeflow-examples :maxdepth: 2 :hidden: 4_examples/overview 4_examples/assignment_example1 4_examples/count_example1 4_examples/combined_example1 4_examples/plasmid_example 4_examples/complex_readstructure_example 4_examples/GSE306816_example 4_examples/GSE293036_example 4_examples/GSE316891_example 4_examples/GSE284330_example 4_examples/GSE325670_example 4_examples/GSE271608_example 4_examples/GSE307247_example .. toctree:: :caption: Tips & Tricks :name: tips-tricks :maxdepth: 1 :hidden: 5_tips/faq .. toctree:: :caption: Project Info :name: project-info :maxdepth: 1 :hidden: 6_info/contributing 6_info/authors 6_info/history 6_info/license