Genome assembly of Histoplasma capsulatum samples
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). Therefore, genome assemblies were generated from Illumina sequencing reads in the SRA/ENA databases.  Genome assemblies from 403 H. capsulatum samples were generated de novo using Shovill version 1.1.0 (https://github.com/tseemann/shovill) using the SPAdes assembler version 3.15.5 using default settings in the Shovill program, with a minimum contig size of 500 nt and minimum coverage of 2x. Assembly metrics (N50 etc) were determined using QUAST 5.0.2. Genome sequences were also generated from single samples of Blastomyces dermatitidis, Blastomyces parvus, Emergomyces (Emmonsia) pasteuriana and Paracoccidioides brasiliensis to serve as outgroups for phylogenetic tree rooting. BUSCO 6.1.0 was used with the ajellomycetaceae_odb12.2 lineage database to estimate completeness. Assemblies and annotations were used for generation of MLST schemes using chewBBACA 3.5.4.
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). Therefore, genome assemblies were generated from Illumina sequencing reads in the SRA/ENA databases.  Genome assemblies from 403 H. capsulatum samples were generated de novo using Shovill version 1.1.0 (https://github.com/tseemann/shovill) using the SPAdes assembler version 3.15.5 using default settings in the Shovill program, with a minimum contig size of 500 nt and minimum coverage of 2x. Assembly metrics (N50 etc) were determined using QUAST 5.0.2. Genome sequences were also generated from single samples of Blastomyces dermatitidis, Blastomyces parvus, Emergomyces (Emmonsia) pasteuriana and Paracoccidioides brasiliensis to serve as outgroups for phylogenetic tree rooting. BUSCO 6.1.0 was used with the ajellomycetaceae_odb12.2 lineage database to estimate completeness. Assemblies and annotations were used for generation of MLST schemes using chewBBACA 3.5.4.