sc2ts-paper

This repository contains all analysis for the preprint A pandemic-scale Ancestral Recombination Graph for SARS-CoV-2

Links

• Live in-browser demo
• Data processing example notebook
• sc2ts homepage
• sc2ts package on PyPi
• sc2ts documentation
• Inferred ARG in tszip format
• Viridian dataset in VCZ format
• UShER Viridian tree tszip format

Repo layout

• The latex directory contains the manuscript
• The viridian_dataset directory contains the Snakemake pipeline for aligning the Viridian consensus sequences and converting to VCF Zarr format.
• The inference directory contains the configuration file used to run primary inference with sc2ts.
• The arg_postprocessing directory contains Snakemake workflow for postprocessing the ARG, and running all major analyses in the paper (RIPPLES, CovRecomb, etc)
• The notebooks directory contains the Jupyter notebooks used to perform analyses, genererate tables and figures in the manuscript.
• The src directory contains a few miscellaneous scripts