Hound: a novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo.

ABSTRACT: Increasing evidence suggests that microbial species have a strong within species genetic heterogeneity. This can be problematic for the analysis of prokaryote genomes, which commonly relies on a reference genome to guide the assembly process. Differences between reference and sample genomes will therefore introduce errors in final assembly, jeopardizing the detection from structural variations to point mutations-critical for genomic surveillance of antibiotic resistance. Here we present Hound, a pipeline that integrates publicly available tools to assemble prokaryote genomes de novo, detect user-given genes by similarity to report mutations found in the coding sequence, promoter, as well as relative gene copy number within the assembly. Importantly, Hound can use the query sequence as a gu

SUBMITTER: Reding C 

PROVIDER: S-EPMC10883467 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature