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arg-needle-lib

This repository contains arg-needle-lib, which implements an ARG data structure and ARG-based analyses such as genealogy-wide association.

Prebuilt CPython wheels are available for Linux (compatible with glibc ≥ 2.28) and macOS (built on macOS 15 for x86_64 and macOS 14 for arm64).

Platform \ CPython ≤3.8 3.9 3.10 3.11 3.12 3.13 3.14
Linux x86_64 ❌ ✅ ✅ ✅ ✅ ✅ ✅
Linux aarch64 ❌ ✅ ✅ ✅ ✅ ✅ ✅
macOS Intel (x86_64) ❌ ✅ ✅ ✅ ✅ ✅ ✅
macOS Apple Silicon (arm64) ❌ ✅ ✅ ✅ ✅ ✅ ✅

Quickstart

Install the Python module from PyPI

Most functionality is available through a Python module which can be installed with:

pip install arg-needle-lib

This Python module is currently available on Linux and macOS.

Documentation

Please see the ARG-Needle manual for all usage instructions and documentation.

License

arg-needle-lib is distributed under the GNU General Public License v3.0 (GPLv3). For any questions or comments on arg-needle-lib, please contact Pier Palamara using <lastname>@stats.ox.ac.uk.

Acknowledgements

arg-needle-lib is developed by (in alphabetical order) Arjun Biddanda, Fergus Cooper, Árni Freyr Gunnarsson, Pier Francesco Palamara, Sinan Shi, Brian C. Zhang, and Jiazheng Zhu.

Reference

If you use this software, please cite:

B. C. Zhang, A. Biddanda, Á. F. Gunnarsson, F. Cooper, P. F. Palamara, Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nature Genetics, 2023.