Welcome to the sfkit CLI documentation!
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The **sfkit CLI** is a collection of command-line interface tools to facilitate privacy preserving and secure genomics analyses with multiple parties.
It serves as a companion to the `sfkit <https://sfkit.org/>`_ website, by providing a command-line interface for users to run *user-configured* studies utilizing their own compute environments.

Contents
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.. toctree::
   :maxdepth: 3

   installation

.. toctree::
   :maxdepth: 1

   tutorial
   tutorial_2

.. toctree::
   :maxdepth: 3

   commands

Related Publications
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Our project has been documented in several research articles. For a more detailed understanding of our work, you can access these articles via the links below:

- `sfkit: a web-based toolkit for secure and federated genomic analysis <https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad464/7184156>`_ (Nucleic Acids Research, 2023): This article provides an overview of the entire sfkit project.
- `Secure Genome-wide Association Analysis Using Multiparty Computation <https://www.nature.com/articles/nbt.4108>`_ (Nature Biotechnology, 2018): This paper introduces the MPC-GWAS workflow.
- `Truly Privacy-Preserving Federated Analytics for Precision Medicine with Multiparty Homomorphic Encryption <https://www.nature.com/articles/s41467-021-25972-y>`_ (Nature Communications, 2021): This paper details the SF-GWAS workflow.
- `Secure and Federated Genome-Wide Association Studies for Biobank-Scale Datasets <https://www.biorxiv.org/content/10.1101/2022.11.30.518537v1>`_ (Preprint): This paper outlines recent enhancements to the SF-GWAS workflow.
- `Realizing private and practical pharmacological collaboration <https://www.science.org/doi/10.1126/science.aat4807>`_ (Science, 2018): This paper introduces the Secure-DTI workflow.

Questions
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For questions or concerns, you can create an issue on the `github repository <https://github.com/hcholab/sfkit/issues>`_ or reach us at `support@sfkit.org <support@sfkit.org>`_.