Database and assemblies to accompany the Afanc paper. This database covers species-level classification of Mycobacteriaceae, mpox, and Plasmodium spp, and lineage/clade level classification of M. tuberculosis, P. falciparum, and mpox clade IIb. All mpox assemblies obtained from GISAID which were used in the database utilised in the paper have been removed, and txt files containing EPI_IDs for the assemblies placed in their taxon directory.