Data and scripts for reproducing the analyses in the hospital microbiome project

This repository contains data and scripts used in our recent manuscript (Chng et al, 2020).

Directory structure

• metadata: Metadata files mapping sequencing IDs to sample information
• output_tables: Data files generated by analysis scripts
• plots: Figures presented in the manuscript
• scripts: R markdown files (with rendered html) for the analysis
• tables: Input data used for generating the figures

Downloading this repository

1. Clone the core component using git

git clone https://github.com/csb5/hospital_microbiome.git

2. Download large datasets using git lfs

cd hospital_microbiome && git lfs pull

Raw data availability

• Raw sequencing data has been uploaded to European Nucleotide Archive
• Assemblies and annotations are available at Figshare
• Source code and software for visualizing the data on 3D models are available on github

Citation

Chng et al. (2020). Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature Medicine (journal version, bioRxiv version).

Contact

Please direct any questions or feedback to Chenhao Li and Niranjan Nagarajan.