A comparison of short- and long-read whole genome sequencing for microbial pathogen epidemiology.

ABSTRACT: Whole genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen. Likewise, variant calling can inform on transmission patterns and evolutionary relationships. Recent improvements in Oxford Nanopore long-read sequencing have made its use attractive for genomic epidemiology. However, the accuracy and optimal strategy for analysis of Nanopore reads remains to be determined. We compared the use of Illumina short reads and Oxford Nanopore long reads for genome assembly and variant calling of phytopathogenic bacteria. We generated short- and long-read datasets for diverse phytopathogenic Agrobacterium strains. We then analyzed these dat

SUBMITTER: Schiffer AM 

PROVIDER: S-EPMC12632941 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature