This repository contains representative code and scripts used to analyze data included in the manuscript "Southern California wastewater RNA viromics and SARS-CoV-2 sequencing." This has now been published in a peer-reviewed journal, Applied and Environmental Microbiology. https://journals.asm.org/doi/10.1128/AEM.01448-21
"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 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.