BioHansel

BioHansel identifies phylogenetically informative single nucleotide polymorphisms (canonical SNPs) in whole genome sequencing (WGS) data using fast k-mer matching and assigns hierarchical genotypes for high-resolution bacterial isolate genotyping.

Key Features:

• k-mer matching: Uses a fast k-mer matching algorithm to map WGS data against canonical SNPs.
• Input types: Accepts raw sequence reads and assembled contigs as input.
• Hierarchical schemas: Applies hierarchically structured canonical SNP genotyping schemas to determine genotypes.
• Supported species: Includes canonical SNP schemas for Salmonella serovars Typhi, Typhimurium, Enteritidis, Heidelberg, and Mycobacterium tuberculosis.
• Custom schemas: Supports user-supplied custom canonical SNP schemas for other organisms.
• Quality assurance: Implements QA checks to identify low-quality data, contaminated datasets, and misidentified organisms.
• Genotype nomenclature: Produces compact, interpretable genotypes that encode a pathogen's position within its population structure.
• Performance: Rapidly types isolates within seconds and operates on modest computing resources.
• Implementation: Implemented in Python 3.

Scientific Applications:

• Infectious disease surveillance and outbreak investigation: Provides high-resolution genotypes to support detection and investigation of outbreaks.
• Public health, food safety, environmental, and agricultural monitoring: Enables routine surveillance and diagnostics across public health, food safety, environmental, and agricultural contexts.
• Source attribution and risk assessment: Supports source attribution, risk assessment, and product recall investigations by linking isolates to population structure.
• Rapid screening and diagnostics: Facilitates rapid screening for priority pathogens and integration into diagnostic workflows.
• Comparative genomics: Enables comparison with circulating and historical strains to identify intervention points and transmission patterns.

Methodology:

BioHansel applies fast k-mer matching to detect canonical SNPs in WGS raw reads or assembled contigs against hierarchically structured SNP schemas, assigns hierarchical genotypes based on detected SNP profiles, supports custom schemas, and performs quality assurance checks to flag low-quality, contaminated, or misidentified datasets.