Katie M.V. Hopkins

OxBreaker is a species-agnostic pipeline for analyzing bacterial and plasmid outbreaks using nanopore sequencing, offering high accuracy and accessibility for real-time genomic surveillance.

This study evaluates Nanopore long-read only genome assembly for clinical Enterobacterales isolates, finding Autocycler with Medaka polishing achieves accuracy comparable to hybrid assemblies.

This paper evaluates the accuracy of bacterial genome reconstruction using Oxford Nanopore R10.4.1 long-read-only sequencing and finds it produces accurate assemblies at 40x depth, competitive with hybrid Illumina-Nanopore assemblies.