ARGprofiler

ARGprofiler performs large-scale analysis of antimicrobial resistance genes (ARGs) and their flanking regions in metagenomic sequencing datasets to characterize ARG presence, abundance, and genetic context.

Key Features:

• Standardized Workflow: Integrates multiple tools and reference databases into a unified, reproducible workflow to promote comparability across metagenomic ARG studies.
• PanRes Database Integration: Uses the PanRes database containing 14,078 unique ARGs as the primary reference for ARG identification.
• Flanking Region Reconstruction: Reconstructs ARG flanking regions using ARGextender by combining KMA and SPAdes for targeted de novo assembly of reads surrounding ARGs.
• Abundance Tables: Produces tables quantifying gene and microbial taxon abundances within metagenomic samples.
• Mash Sketches for Fast Comparisons: Generates Mash sketches to enable rapid similarity searches and comparisons between sequencing runs.
• Snakemake Workflow Management: Implements the pipeline under Snakemake to provide a modular, rule-based workflow structure for scalable execution.

Scientific Applications:

• Epidemiological Studies: Characterizes the distribution and evolution of antimicrobial resistance across populations and environments.
• Environmental Monitoring: Monitors ARG prevalence in ecosystems such as soil, water, and waste treatment facilities.
• Clinical Research: Analyzes patient microbiomes and hospital environments to identify potential sources and contexts of resistant pathogens.

Methodology:

Processes raw sequencing reads through read processing and quality control; identifies ARGs using the PanRes database; assembles flanking regions with ARGextender (KMA + SPAdes) for targeted de novo assembly; generates abundance and diversity tables; and creates Mash sketches for dataset comparison.