confindr cgMLST scheme for Campylobacter

Novel ConFindr cgMLST scheme for Campylobacter spp. The resulting scheme has 40 independent loci. For usage, download the scheme and add it to the directory of your ConFindr databases. For more information on confinder, see https://olc-bioinformatics.github.io/ConFindr/usage/#using-schemes-other-than-rmlst

Details:
The scheme was generated following the ConFindr script create_genus_specific_db.py (https://github.com/OLC-Bioinformatics/ConFindr/tree/master/confindr_src) with the modification that the minimum genome size was set to 1Mbp instead of 2Mbp. In brief, the script downloads all complete Campylobacter spp. genomes (354 complete genomes from 33 different Campylobacter species) from NCBI RefSeq. It then performs pairwise Nucleotide BLAST with a set of reference genes in order to identify suitable genes for the cgMLST scheme. The reference genes were obtained from the Campylobacter reference strain Campylobacter jejuni subsp. jejuni NCTC 11168 (accession: NC_002163.1). All 1573 genes were renamed and extracted into single files.