poojasgupta / wastewater-covidseq

Wastewater sequencing data analysis

Wastewater genomic surveillance captures early detection of Omicron in Utah

This repository contains the R code used in the analysis and visualization of genomic surveillance data of the Omicron variant of SARS-CoV-2 in Utah. The manuscript associated with this code is titled "Wastewater genomic surveillance captures early detection of Omicron in Utah" and is available at https://www.medrxiv.org/content/10.1101/2022.11.24.22282643v2

Data preprocessing

The R code reads a raw data file, formats the dates, filters the data based on the study period, and groups the lineages for further analysis. It also reads a corrected lineage abundance data file and applies additional filtering and grouping.

Analysis

The analysis focuses on summarizing the data, grouping lineages, and creating visualizations. The code includes the creation of a detailed lineage plot for the supplementary materials and a lineage plot for the main text.

Visualizations

Visualizations created using ggplot2 include:

1. Detailed lineage plot (Supplementary)
2. Bar plot for Delta and Omicron lineages
3. Bar plot for Omicron lineages

Dependencies

The following R packages are required to run the code:

• dplyr
• tidyverse
• ggplot2
• ggpubr
• ggthemes
• gridExtra
• lubridate
• tibbletime
• scales
• viridis
• patchwork
• broom.mixed

File Structure

• R code: The main R code file is provided in this repository.

Usage

To run the code, clone the repository and ensure that the required R packages are installed. Open the R script file and update the file paths to match the location of the data files on your system. Run the script to generate the visualizations and output data file.

Citation

If you use this code or data, please cite the associated manuscript:

Wastewater genomic surveillance captures early detection of Omicron in Utah