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sc2ts

Sc2ts stands for "SARS-CoV-2 tree sequence" (pronounced "scoots" optionally) and consists of

  1. A method to infer Ancestral Recombination Graphs (ARGs) from SARS-CoV-2 genome sequence data at pandemic scale.
  2. A lightweight wrapper around tskit Python APIs specialised for the output of sc2ts which enables efficient node metadata access.
  3. 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 an inferred ARG.