Merge branch 'master' of https://github.com/CSB5/hospital_microbiome

README.md

@@ -1,12 +1,12 @@
 # Data and scripts for reproducing the analyses
 
-This repository contains data and scripts used in the manuscript titled "Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment".
+This repository contains data and scripts used in our recent manuscript ([Chng *et al*, 2020](#citation)).
 
 ## Directory structure
 
- - [metadata](metadata): Metadata files mapping sequencing IDs to site information
+ - [metadata](metadata): Metadata files mapping sequencing IDs to sample information
  - [output_tables](output_tables): Data files generated by analysis scripts
- - [plots](plots): Figures used in the manuscript
+ - [plots](plots): Figures presented in the manuscript
  - [scripts](scripts): R markdown files (with rendered html) for the analysis
  - [tables](tables): Input data used for generating the figures
 
@@ -25,9 +25,15 @@ cd hospital_microbiome && git lfs pull
 ## Raw data availability
 
  - Raw sequencing data has been uploaded to [European Nucleotide Archive](https://www.ebi.ac.uk/ena/data/view/PRJEB31632)
- - Assemblies and annotations are available at [figshare](https://ndownloader.figshare.com/files/17290511)
+ - Assemblies and annotations are available at [Figshare](https://figshare.com/articles/Cartography_of_opportunistic_pathogens_and_antibiotic_resistance_genes_in_a_tertiary_hospital_environment/11683350)
+ - Source code and software for visualizing the data on 3D models are available on [github](https://github.com/CSB5/hospital_microbiome_explorer)
 
 ## Citation
 
-Chng, Li, Bertrand, et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. BioRxiv (2019)
+Chng *et al*. (2020). Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. *In press*.
 
+Note: A self-archived version of the manuscript is available at [BioRxiv](https://www.biorxiv.org/content/10.1101/644740v2).
+
+## Contact
+
+Please direct any questions or feedback to [Chenhao Li](mailto:[email protected]) and [Niranjan Nagarajan](mailto:[email protected]).