STing

STing performs k-mer–based genomic profiling and gene detection directly from next-generation sequencing (NGS) raw reads to support molecular epidemiology and surveillance of antimicrobial resistance and virulence factors.

Key Features:

• k-mer search strategy: Uses a k-mer–based algorithm to identify alleles and genes from sequencing reads.
• Raw-read analysis without preprocessing: Operates directly on NGS raw reads without requiring quality control, assembly, or alignment.
• Multilocus sequence typing (MLST) and genome-scale typing: Supports standard MLST schemes and larger genome-scale typing projects.
• Antimicrobial resistance and virulence gene detection: Performs rapid automated detection of antimicrobial resistance genes and virulence factors from reads.
• Reduced computational overhead and speed: Bypasses time-consuming preparatory processes to lower computational resource usage and accelerate analysis.
• Accuracy and benchmarking: Demonstrated superior performance in speed and precision in comparative studies against six widely used genome-based molecular typing programs.

Scientific Applications:

• Molecular epidemiology: Enables rapid genomic profiling of microbial pathogens for outbreak investigation and transmission studies.
• Sequence typing: Produces MLST and genome-scale typing results for strain characterization.
• Antimicrobial resistance surveillance: Detects antimicrobial resistance genes directly from sequencing reads for public health monitoring.
• Virulence factor surveillance: Identifies virulence-associated genes from raw NGS data.
• Genomic profiling of pathogens: Provides allele- and gene-level profiles to support pathogen characterization and surveillance.

Methodology:

Implements a k-mer search strategy applied to NGS raw reads to detect alleles and genes without performing quality control, assembly, or alignment.