sc2ts 
Sc2ts stands for "SARS-CoV-2 tree sequence" (pronounced "scoots" optionally) and consists of
- A method to infer Ancestral Recombination Graphs (ARGs) from SARS-CoV-2 genome sequence 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.
For details on the software, please see the online documentation. For information on the method and an inferred ARG, please see this preprint:
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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Release files for sc2ts 1.1.0
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Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sc2ts-1.1.0.tar.gz | 1.9 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sc2ts-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 2.1 MB
Release files / sc2ts-1.1.0.tar.gz
| Download URL | sc2ts-1.1.0.tar.gz |
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| Size | 1.9 MB |
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| Download URL | sc2ts-1.1.0-py3-none-any.whl |
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| Size | 118.6 kB |
| Tags | Python 3 |
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