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README.md

Extracting validation data from the Blackwell collection

This process extracts the MLST validation data from the Blackwell collection as outlined in the manuscript.

  1. Download the meta-data JSON (https://figshare.com/ndownloader/files/26578377)
  2. Run the species.py application (python species.py --help) on the JSON file, this will produce a summary of the meta-data including MLST (species_data.tsv), a file for all FTP addresses (species_ftp.tsv) and count data for all species (Bracken, species_counts.tsv)
  3. Download the assemblies from the FTP addresses for a species of interest, these can be used for sketch construction. Genotype files can be constructed from subsets of the species_data.tsv file for the assemblies included in the sketch.
  4. You may want to run a check on the order and congruence between sketch and genotype file. Commands for sketch construction are outlined in the local sketches and genotype files sections of the documentation.