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jeromekelleher merged 1 commit into from
Jun 8, 2026
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Add citation for the latest v3 preprint #611

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5 changes: 2 additions & 3 deletions README.md
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Expand Up @@ -6,7 +6,6 @@ Sc2ts stands for "SARS-CoV-2 tree sequence" (pronounced "scoots" optionally) and
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 an inferred ARG.
For details on the software, please see the online [documentation](https://tskit.dev/sc2ts/docs). For information on the method and an inferred ARG, please see this [preprint](https://www.biorxiv.org/content/10.1101/2023.06.08.544212v3):

> 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
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