Highly scalable inference of ancestral recombination graphs (ARGs)

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Project description

Threads

This software implements the Threads algorithm, described in

Á. F. Gunnarsson, J. Zhu, B. C. Zhang, Z. Tsangalidou, A. Allmont, P. Palamara. A scalable approach for genome-wide inference of ancestral recombination graphs. bioRxiv, 2024.

The user manual for threads can be found here.

Installation

pip install threads_arg

threads Release Notes

[0.2.1] - 2025-06-03

Added

VCF conversion backwards compatibility (#76)
Add Linux ARM platform to Python wheels (#82)

[0.2.0] - 2025-04-29

Added

Optimised imputation (#28)
Variant mapping (#38)
Upgrade to numpy 2.0 (#39)
Consistent SHAPEIT format for regions (#42)
Ability to write impute output directly to stdout (#42)
Allele age estimation and data consistency (#51)

Fixed

Fix os.sched_getaffinity macOS error (#49)

[0.1.0] - 2024-07-04

Added

Initial version of threads

Project details

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Release history Release notifications | RSS feed

This version

0.2.1

Jun 3, 2025

0.2.0

Apr 29, 2025

0.1.0

Jul 4, 2024

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threads-arg 0.2.1

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[0.2.1] - 2025-06-03

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