Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.

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 u

SUBMITTER: Labbe G 

PROVIDER: S-EPMC8715432 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature