Supplemental Information for Emmen et al. 2024

Overview

This repository contains supplemental files associated with Emmen et al. 2024, SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests, including:

1. Data files used to generate figures (see data/)
2. R scripts used to generate figures associated with each data file (see scripts/)
3. The PDF-formatted figures themselves (see figures/)
4. instructions on running nf-core/viralrecon with the settings used for the manuscript (see viralrecon_setup/)

This README will also go over how to use the scripts to reproduce the figures.

Reproducing Figures

The two R scripts in this repo, scripts/plot_ct_by_n_count.R and scripts/plot_test_counts.R, can be used to reproduce the Ct-value and test count figures in Emmen et al. 2024. To do so, make sure R is installed. In an R console, make sure the tidyverse and extrafonts libraries are installed globally with the following:

install.packages("tidyverse")
install.packages("extrafonts")

Once both installations have finished, the scripts can be run like so:

Rscript scripts/plot_ct_by_n_count.R
Rscript scripts/plot_test_counts.R

This will regenerate the figures in figures/.

Setting up nf-core/viralrecon

Emmen et al. 2024 uses the open-source pipeline nf-core/viralrecon to perform its bioinformatics. Comprehensive instructions on setting up viralrecon with the same settings the manuscript used can be read at viralrecon_setup/README.md.

Citation

Coming soon!