danielkim617/E_coli_strain_tracking

Scripts and code for analyzing E. coli strain-sharing patterns among humans, animals, and the environment in urban slum communities in Kenya. # E. coli Strain-Sharing Analysis using PIC-seq This repository contains scripts and codes for analyzing PIC-seq data to study *E. coli* strain-sharing patterns among humans, animals, and the environment in urban slum communities in Kenya. ## Folder Structure ### `benchmarking` - Contains scripts and source files for performance comparisons across different sequence assembly approaches. ### `R_script` - Contains scripts and folders for data analysis and figure generation, including: - **`0-config.R`**: Sets configurations for running the analysis scripts. - **`0-functions.R`**: Contains core functions used for the analysis. - **`analysis` folder**: Includes R scripts for data analysis. - **`figure` folder**: Includes scripts for plotting figures. ---