Sc2ts stands for "SARS-CoV-2 tree sequence" (pronounced "scoots" optionally) and consists of
- A method to infer Ancestral Recombination Graphs (ARGs) from SARS-CoV-2 genome sequence data at pandemic scale.
- A lightweight wrapper around tskit Python APIs specialised for the output of sc2ts which enables efficient node metadata access.
- A lightweight wrapper around Zarr Python which enables convenient and efficient access to the full Viridian dataset (alignments and metadata) in a single file using the VCF Zarr specification.
For details on the software, please see the online documentation. For information on the method and an inferred ARG, please see this preprint:
Shing H. Zhan, Yan Wong, Anastasia Ignatieva, Katherine Eaton, Isobel Guthrie, Benjamin Jeffery, Duncan S. Palmer, Carmen Lia Murall, Sarah P. Otto, and Jerome Kelleher (2025) A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2. bioRxiv: 2023.06.08.544212; doi: https://doi.org/10.1101/2023.06.08.544212