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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">
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Sc2ts stands for "SARS-CoV-2 to tree sequence" (pronounced "scoots" optionally)
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and consists of
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Sc2ts stands for "SARS-CoV-2 tree sequence" (pronounced "scoots" optionally) and consists of
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1. A method to infer Ancestral Recombination Graphs (ARGs) from SARS-CoV-2
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data at pandemic scale
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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
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access.
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3. A lightweight wrapper around [Zarr Python](https://zarr.dev) which enables
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convenient and efficient access to the full Viridian dataset (alignments and metadata)
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in a single file using the [VCF Zarr specification](https://doi.org/10.1093/gigascience/giaf049).
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1. A method to infer Ancestral Recombination Graphs (ARGs) from SARS-CoV-2 genome sequence data at pandemic scale.
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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.
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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).
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Please see the online [documentation](https://tskit.dev/sc2ts/docs) for details
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on the software
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and the [preprint](https://www.biorxiv.org/content/10.1101/2023.06.08.544212v3)
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for information on the method and the inferred ARG.
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on the software and the [preprint](https://www.biorxiv.org/content/10.1101/2023.06.08.544212v3)
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for information on the method and an inferred ARG.
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