Fig. 1

Schematic design of Maast. Maast consists of four major components. a Tag genomes and centroid genomes are selected based on Mash distances. A novel algorithm, called DynaCC, is used to automatically choose the genome clustering threshold based on each species’ level of genomic redundancy (see the “Methods” section). b A panel of common SNPs is constructed for each species using multiple whole-genome alignment. c SNPs in non-tag genomes or other input genomes are genotyped using single whole-genome alignment. d SNPs in short reads are genotyped using k-mer exact matching