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Working group bacterial genomics, part 2

  1. create a whole genome schema based on the full set of genomes using chewBBACA CreateSchema and call the alleles for each sample using chewBBACA AlleleCall
  2. test the quality of the genomes in term of allele calling using chewBBACA TestGenomeQuality
  3. extract the core genome MLST allele profiles from the dataset using chewBBACA ExtractCgMLST

will you include all the genomes? would you exclude certain loci (eg. reapted loci)? at which level you will perform your cgMLST analysis (100%, 99%, 95%, etc.)?

  1. make sure that the cgMLST.tsv file contains the samples name in the first column as written in the TSV above produced with Abrigate. If not, adapt either the cgMLST.tsv or the TSV file.