Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel

BioHansel performs high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. Using modest computing resources, BioHansel efficiently types isolates from raw sequence reads or assembled contigs in a matter of seconds, making it attractive for use by public health, food safety, environmental, and agricultural authorities that wish to apply WGS methodologies for their surveillance, diagnostics, and research programs. BioHansel currently provides canonical SNP genotyping schemas for four prevalent Salmonella serovars: Typhi, Typhimurium, Enteritidis and Heidelberg, as well as a schema for Mycobacterium tuberculosis. Users can also supply their own schemas for genotyping other organisms. Its quality assurance system assesses the validity of the genotyping results and can identify low quality data, contaminated datasets, and misidentified organisms. BioHansel is targeted to support surveillance, source attribution, risk assessment, diagnostics, and rapid screening for public health purposes, such as product recalls. BioHansel is an open source application with packages available for PyPI, Conda, and the Galaxy workflow manager. In summary, BioHansel performs efficient, rapid, accurate, and high-resolution classification of bacterial genomes from sequence reads or assembled contigs on standard computing hardware. BioHansel is suitable for use as a general research tool as well as in fully operationalized WGS workflows at the front lines of infectious disease surveillance, diagnostics, and outbreak investigation and response.