This is the repository for the code that produces analysis and figures in the preprint Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2 (https://doi.org/10.1101/2023.06.08.544212). See our virological.org post at https://virological.org/t/towards-pandemic-scale-ancestral-recombination-graphs-of-sars-cov-2/936 for a brief summary.
The main sc2ts software itself exists in a separate repository: https://github.com/jeromekelleher/sc2ts
Jupyter notebooks to perform the analysis of the "Wide" and "Long" ARGs described in the preprint are present in
the notebooks directory.
The Wide and Long ARGs themselves, in compressed tskit format, which are required for most of the analysis, are subject to GISAID distribution conditions, hence we have not placed them online. They are available by request from the authors.
To cite the preprint, please use:
S. H. Zhan, A. Ignatieva, Y. Wong, K. Eaton, B. Jeffery, D. S. Palmer, C. L. Murall, S. Otto, and J. Kelleher. (2023) Towards pandemic-scale ancestral recombination graphs of SARS-CoV-2. bioRxiv 2023.06.08.544212; doi: https://doi.org/10.1101/2023.06.08.544212