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jeromekelleher merged 1 commit into from
Jan 27, 2026
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Minor edits to README #589

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18 changes: 6 additions & 12 deletions README.md
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# sc2ts <img align="right" width="145" height="90" src="https://raw.githubusercontent.com/tskit-dev/sc2ts/main/docs/sc2ts.png">

Sc2ts stands for "SARS-CoV-2 to tree sequence" (pronounced "scoots" optionally)
and consists of
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
data at pandemic scale
2. A lightweight wrapper around [tskit Python APIs](https://tskit.dev/tskit/docs/stable/python-api.html) specialised for the output of sc2ts which enables efficient node metadata
access.
3. A lightweight wrapper around [Zarr Python](https://zarr.dev) which enables
convenient and efficient access to the full Viridian dataset (alignments and metadata)
in a single file using the [VCF Zarr specification](https://doi.org/10.1093/gigascience/giaf049).
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](https://tskit.dev/tskit/docs/stable/python-api.html) specialised for the output of sc2ts which enables efficient node metadata access.
3. A lightweight wrapper around [Zarr Python](https://zarr.dev) which enables convenient and efficient access to the full Viridian dataset (alignments and metadata) in a single file using the [VCF Zarr specification](https://doi.org/10.1093/gigascience/giaf049).

Please see the online [documentation](https://tskit.dev/sc2ts/docs) for details
on the software
and the [preprint](https://www.biorxiv.org/content/10.1101/2023.06.08.544212v3)
for information on the method and the inferred ARG.
on the software and the [preprint](https://www.biorxiv.org/content/10.1101/2023.06.08.544212v3)
for information on the method and an inferred ARG.