Welcome to the sfkit CLI documentation!

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 website, by providing a command-line interface for users to run user-configured studies utilizing their own compute environments.

Contents

• Installation
  • pip
  • tar.gz Release
  • docker
  • Building the Docker Image Locally

• Tutorial 1 (Quick test for one user)
• Tutorial 2 (Examples with two users)

• Commands
  • Positional Arguments
  • Sub-commands
    • auth
    • networking
    • generate_keys
    • register_data
    • run_protocol
    • server
    • client
    • run (all)

Related Publications

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 (Nucleic Acids Research, 2023): This article provides an overview of the entire sfkit project.

• Secure Genome-wide Association Analysis Using Multiparty Computation (Nature Biotechnology, 2018): This paper introduces the MPC-GWAS workflow.

• Truly Privacy-Preserving Federated Analytics for Precision Medicine with Multiparty Homomorphic Encryption (Nature Communications, 2021): This paper details the SF-GWAS workflow.

• Secure and Federated Genome-Wide Association Studies for Biobank-Scale Datasets (Preprint): This paper outlines recent enhancements to the SF-GWAS workflow.

Questions

For questions or concerns, you can create an issue on the github repository or reach us at support@sfkit.org.