1. Uploading and selecting data
You can choose to upload and view your own data or explore the built in datasets described in the preprint Lam, MMC. et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications (2021). These include the Global dataset (13,156 publicly available Klebsiella genomes with matched isolate metadata) and the EuSCAPE dataset (pan-European genomic surveillance data from Nov 2013 to May 2014 with matched isolate metadata and antimicrobial minimum-inhibitory concentrations, originally described here). You can select these datasets by clicking the corresponding buttons in the left side panel.
Upload your own data via the the Upload data buttons at the top of the left side panel. There are three possible input data files:
- Kleborate output (required): This is the raw .txt output file from Kleborate, either generated locally or downloaded from PathogenWatch.
- Metadata (optional): This file contains additional information for the isolates corresponding to the genomes in the Kleborate output e.g. year of collection, sample type, country of collection. The file must contain a column called 'strain' that has values matching exactly with the names of the genomes in the Kleborate output (one per row). If available, the year of collection should be provided in a column called 'Year', but all other column names can be chosen by the user. The file must be in comma-separated format (csv).
- MIC table (optional): This file contains antimicrobial minimum inhibitory concentrations (MICs) for the isolates corresponding to the genomes in the Kleborate output. The file must contain a column called 'strain' that has values matching exactly with the names of the genomes in the Kleborate output (one per row). All other columns should contain only MIC data. The file must be in comma-separated format (csv).
The side panel also shows a data summary table that is populated after data upload / selection. It shows the total number of unique species and sequence types (STs) in the data set as well as the mean virulence and resistance scores.
