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From: Typing methods based on whole genome sequencing data

Method Approach Reference Primary result Secondary result
cgMLST Alignment to scheme of core genes Set of allele sequences for set of core genes Allele distance matrix Minimum-spanning tree
wgMLST Alignment to scheme of core and accessory genes Set of allele sequences for set of core and accessory genes Allele distance matrix Minimum-spanning tree
SNP Mapping to reference Closely related reference genome Core SNP alignment, SNP distance matrix Neighbor-joining tree
Maximum- likelihood tree
split K-mer based SNP detection Pairwise K-mer comparison No reference Core SNP alignment, SNP distance matrix Neighbor-joining tree
MinHash Pairwise MinHash comparison and clustering No reference MinHash distances, clustering information Neighbor-joining tree