This repository contains representative code and scripts used to analyze data included in the manuscript "Longitudinal sequencing and variant detection of SARS-CoV-2 across Southern California wastewater." which is now accepted for publication at Applied Microbiology.

A preprint of the manuscript can be found here: https://www.medrxiv.org/content/10.1101/2023.04.14.23288559v1.

"github_R_scripts" contains R scripts used to analyze the data and generate figures.

"github_hpc_scripts" contains shell scripts used to analyze the data on the UC Irvine High Performance Community Computing Cluster (UCI HPC3). Each underlying program was either loaded as an HPC3 module or activated via conda installations.

This page will be continuously updated with links to the manuscript, data, and code as needed.