NanoCore

NanoCore calculates and visualizes core-genome multilocus sequence typing (cgMLST) sample distances directly from unassembled Nanopore reads for bacterial genomic surveillance and outbreak detection in healthcare facilities.

Key Features:

• Nanopore read analysis: Processes unassembled Nanopore reads in FASTQ format without requiring prior genome assembly.
• cgMLST distance calculation: Computes core-genome multilocus sequence typing-like pairwise sample distances.
• Distance visualization: Generates visualizations of cgMLST sample distances for interpretation of isolate relatedness.
• Illumina data support: Analyzes Illumina sequencing data in addition to Nanopore data.
• Hybrid mode: Enables analysis of data sets containing both Nanopore-only and Illumina-only isolates simultaneously.
• Mapping and variant calling: Implements a mapping, variant calling, and multilevel filtering strategy for distance calculation.
• Computational efficiency: Completes analysis of a 24-isolate data set in less than 15 hours of wall time on a workstation.

Scientific Applications:

• Genomic surveillance: Supports early detection of pathogen transmission in healthcare facilities to reduce patient harm.
• Outbreak detection: Identifies closely related bacterial isolates to detect silent outbreaks of healthcare-associated infections.
• MRSA surveillance: Validates near-identical pairwise distances to gold standard methods for methicillin-resistant Staphylococcus aureus.
• VRE surveillance: Validates near-identical pairwise distances to gold standard methods for vancomycin-resistant Enterococcus faecium.
• Transmission chain analysis: Enables improved understanding of pathogen transmission pathways between patients and locations.

Methodology:

NanoCore implements a mapping, variant calling, and multilevel filtering strategy to calculate cgMLST-like distances directly from unassembled reads.