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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
  1. 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.

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