ArticleMicrobial genomics2021
Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Phenotypic and phylogenomic characterization of Lactococcus garvieae isolates from rainbow trout (Oncorhynchus mykiss) in Türkiye.Veterinary research communications · 2026Article
- Genomic and epidemiological identification of Pseudomonas aeruginosa transmission chains and in hospital ICUs.Genome biology · 2026Article
- Genetic Diversity and Molecular Epidemiology ofPathogens (Basel, Switzerland) · 2026Article
- Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi.Genome medicine · 2025Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Characterization of Mycobacterium orygis, Mycobacterium bovis, and Mycobacterium caprae Infections in Humans in Western Canada.The Journal of infectious diseases · 2024Article
- Average Nucleotide Identity and Digital DNA-DNA Hybridization Analysis Following PromethION Nanopore-Based Whole Genome Sequencing Allows for Accurate Prokaryotic Typing.Diagnostics (Basel, Switzerland) · 2024Article
- Mutations inAntibiotics (Basel, Switzerland) · 2024Article
- Evaluation of Whole Genome Sequencing-Based Predictions of Antimicrobial Resistance to TB First Line Agents: A Lesson from 5 Years of Data.International journal of molecular sciences · 2024Article
- Whole genome sequencing-based identification of human tuberculosis caused by animal-lineageJournal of clinical microbiology · 2023Article
- Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196.BMC genomics · 2022Article
- How much do smear-negative patients really contribute to tuberculosis transmissions? Re-examining an old question with new tools.EClinicalMedicine · 2022Article
- Generalizable characteristics of false-positive bacterial variant calls.Microbial genomics · 2021Article
Corrections and comments
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. The BioHansel tool was developed to provide an organism-agnostic tool for hierarchical SNP-based genotyping. The tool identifies split k-mers that distinguish predefined lineages in whole genome sequencing (WGS) data using SNP-based genotyping schemes. BioHansel uses the Aho-Corasick algorithm to type isolates from assembled genomes or raw read sequence data in a matter of seconds, with limited computational resources. This makes BioHansel ideal for use by public health agencies that rely on WGS methods for surveillance of bacterial pathogens. Genotyping results are evaluated using a quality assurance module which identifies problematic samples, such as low-quality or contaminated datasets. Using existing hierarchical SNP schemes for
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