Sc2ts stands for "SARS-CoV-2 to tree sequence" (pronounced "scoots" optionally) and consists of
- A method to infer Ancestral Recombination Graphs (ARGs) from SARS-CoV-2 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.
Please see the online documentation for details on the software and the preprint for information on the method and the inferred ARG.