Enterobase cgMLST scheme for Salmonella enterica prepared for usage with chewBBACA

cgMLST scheme used for analysis in https://www.frontiersin.org/articles/10.3389/fmicb.2021.649517

The cgMLST scheme for Salmonella was downloaded on June 11, 2018 from Enterobase (http://enterobase.warwick.ac.uk/) using the web API. As the sequencing data of the study was published at a later date, this ensured that the downloaded cgMLST scheme did not already contain allele numbers from our dataset. From the 3002 loci in Enterobase, 3000 loci can be utilized in chewBBACA, as it is required that that all loci represent a coding sequence.

The command for preparing the scheme was:

chewBBACA.py PrepExternalSchema -i referenced/Enterobase_Senterica/fasta/ --cpu 16 -v