Data repository for the manuscript A Novel Technique to Characterize Klebsiella pneumoniae Populations Indicates that Mono-Colonization is Associated with Risk of Infection

A Novel Technique to Characterize Klebsiella pneumoniae Populations Indicates that Mono-Colonization is Associated with Risk of Infection Source data and code for the associated manuscript Hi there! Thanks for taking a look at this. This repository is intended to store R files and raw data files associated with the above project. The goal of this repository is to provide open access to the analysis performed for the above project, such that it can be replicated by any end-user. If you decide to run this analysis yourself, make sure to change all of the directories! The batch data processing file for mothur is: mothur_processing_mixed.batch An example output logfile from mothur is: mothur.1739469754.logfile The sample metadata files are: case_control_metadata.xlsx mixed_status.xlsx The raw analysis files are: final_mixed_col.opti_mcc.0.03.cons.taxonomy final_mixed_col.opti_mcc.count.summary final_mixed_col.opti_mcc.shared NOTE: These files are direct outputs from mothur. All file generation can be replicated by re-running the batch files above with raw read files from PRJNA1439784. The R script for data processing and analysis is: mixed_col_otu_analysis.R