The identification and annotation of nucleotide variants, including insertions/deletions and single nucleotide polymorphisms (SNPs), from whole genome sequence data is important for studies of bacterial evolution, comparative genomics, and phylogeography. The in Silico Genotyper (ISG) represents a parallel, tested, open source tool that can perform these functions and scales well to thousands of bacterial genomes. ISG is written in Java and requires MUMmer (Delcher, et al., 2003), BWA (Li and Durbin, 2009), and GATK (McKenna, et al., 2010) for full functionality. The source code and compiled binaries are freely available from https://github.com/TGenNorth/ISGPipeline under a GNU General Public License. Benchmark comparisons demonstrate that ISG is faster and more flexible than comparable tools.

5Whole genome sequencing (WGS) of bacteria is becoming standard practice is much more flexible in terms of data input types, job management systems, 2 5 diversity of supported tools, and output formats. We also demonstrate differences in results based on the choice of the reference genome and choice of inferring method and can be obtained from tgennorth.github.io/NASP.

7High-throughput comparative genomics has changed our view of bacterial 8 evolution and relatedness. Many genomic comparisons, especially those 9 regarding the accessory genome that is variably conserved across strains in a

Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and C. posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation was made available. In the current study, the genome of the Silveira strain was sequenced using Single Molecule Real Time Sequencing (SMRT) PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (transversion, translocation, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.