arg-needle

arg-needle

This repository contains arg-needle, which implements the ARG inference algorithms ARG-Needle and ASMC-clust.

Quickstart

Install the Python module from PyPI

The Python module can be installed with:

pip install arg-needle

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

Acknowledgements

arg-needle is developed by Brian C. Zhang with support from Fergus Cooper, Árni Freyr Gunnarsson, and Pier Francesco Palamara.

Reference

If you use this software, please cite:

Biobank-scale inference of ancestral recombination graphs enables genealogy-based mixed model association of complex traits. B. C. Zhang, A. Biddanda, P. F. Palamara. bioRxiv. November 2021.

arg-needle Release Notes

v1.0.3 (2023-08-30)

• ASMC decoders can now take a genetic map file with a specified non-default location.
• ASMC decoders no longer require genetic positions to be strictly increasing: adjacent identical positions are now acceptable.

v1.0.2 (2023-05-25)

Fix default values for sequencing in arg_needle script.

v1.0.1 (2023-03-17)

Bug fix for running build_arg_simulation with ASMC-clust.

v1.0.0 (2023-03-10)

Initial PyPI release of arg-needle.