https://github.com/tskit-dev/sc2ts

ARG inference and analysis utilities for pandemic-scale SARS-CoV-2 data
https://github.com/tskit-dev/sc2ts

args sars-cov-2 tskit

Last synced: about 2 months ago
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ARG inference and analysis utilities for pandemic-scale SARS-CoV-2 data

• Host: GitHub
• URL: https://github.com/tskit-dev/sc2ts
• Owner: tskit-dev
• License: gpl-3.0
• Created: 2022-05-11T08:25:52.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2026-03-03T17:00:31.000Z (about 2 months ago)
• Last Synced: 2026-03-04T04:22:58.245Z (about 2 months ago)
• Topics: args, sars-cov-2, tskit
• Language: Python
• Homepage:
• Size: 3.9 MB
• Stars: 5
• Watchers: 5
• Forks: 4
• Open Issues: 25
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# 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](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.