Carlos RedingHi everyone ๐
If you are thinkging about using #nanopore for genomic surveillance in #hospitals, but don't have the #bioinformatics nor command-line skills, don't let that put you off.
'Modernising Medical Microbiology', at @NDMOxford in #Oxford, has developed `OxBreaker': a graphical tool that can help identify budding #outbreaks by #healthcare professionals without having to upload your data to external servers and compromise patient privacy. Worth a read ๐
OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing
Real-time genomic surveillance may mitigate the spread of health-care-associated infections, but whole-genome sequencing costs and the need for specialised expertise constrain its wide implementation in public health. Here we present โ OxBreaker โ, an automated and species-agnostic pipeline optimised for the high-resolution analysis of bacterial and plasmid genomes sequenced via Oxford Nanopore Technologies (ONT). โ OxBreaker โ streamlines the transition from raw reads to phylogenetic inference through automated reference selection and high-accuracy variant calling. It is accessible via a graphical user interface (GUI) that can be easily installed locally and operated by non-specialists. Benchmarking against technical and biological replicates of high-priority pathogens demonstrates high accuracy, with false positive variant rates reduced to 0โ4 single-nucleotide polymorphisms (SNPs) for common species. We further validated the pipeline by accurately characterising previously published clonal and plasmid-mediated outbreaks, reproducing established phylogenies with improved accessibility. By providing a stable, scalable, open-source offline-compatible solution that matches the resolution of short-read platforms while maintaining the speed of long-read technology, โ OxBreaker โ is designed to facilitate the adoption of local, real-time genomic surveillance for frontline infection prevention and control. ### Competing Interest Statement The authors have declared no competing interest. NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, NIHR207397 NIHR Biomedical Research Centre, Oxford, GB
nf-core
PuckerLab
de.NBI & ELIXIR Germany
Mihail Zdravkov
Jonathan Haars
Kuba.Sawicki