Genome sequence- and annotation-based multilocus sequence typing (MLST) schemes for the fungal pathogen Histoplasma capsulatum

Histoplasma capsulatum is an important fungal pathogen of humans. While genome sequencing has been used for H. capsulatum epidemiology studies, most of these studies are in the form of Illumina reads without an accompanying genome assembly. This limits the development of applications based on genome assemblies, such as genome-based multilocus sequence typing (MLST). Firstly, 403 genome assemblies were generated from Illumina sequencing reads in the SRA/ENA databases. These genome sequences were used to generate MLST schemes with chewBBACA 3.5.4, based on whole genome sequences (wgMLST), NCBI-obtained annotations (annMLST) and annotations obtained with Funannotate 1.8.17 (fanMLST), with 300 and 500 nt minimum ORF length. This archive contains the 6 MLST schemes for chewBBACA 3.5.4, the Prodigal training files and the Supplementary Tables associated with the manuscript submitted.