ARGem

ARGem performs detection, assembly, annotation, and characterization of antibiotic resistance genes (ARGs) and mobile genetic elements from metagenomic short-read DNA sequencing for environmental surveillance.

Key Features:

• Full-service analysis pipeline: Performs data processing, assembly, and annotation of metagenomic short-read DNA sequencing data.
• Metadata capture and harmonization: Captures and harmonizes sample metadata to support comparability across projects and monitoring efforts.
• Efficient short-read assembly: Implements short-read assembly optimized for reasonable runtime to enable accurate ARG annotation.
• Comprehensive annotation databases: Uses extensive databases for antibiotic resistance genes (ARGs) and mobile genetic elements for gene annotation.
• Expandable analytical tools: Provides statistical analyses and network analysis capabilities for downstream interpretation.
• Advanced visualization techniques: Supports visualization of co-occurrence and correlation networks, including output compatible with Cytoscape.
• Scalability via cloud computing: Can leverage cloud computing resources to scale throughput for larger projects.

Scientific Applications:

• Environmental surveillance of ARGs: Monitoring prevalence and spread of antibiotic resistance genes in environmental samples.
• Aquatic metagenome analysis: Characterizing ARGs and mobile genetic elements in aquatic metagenomes.
• Comparative monitoring across projects: Enabling harmonized comparisons of ARG prevalence across studies through metadata harmonization.
• Ecological studies of microbiomes: Investigating ARG distribution and dynamics in soil, water bodies, and animal microbiomes.

Methodology:

Integrates data processing, short-read assembly, annotation against ARG and mobile genetic element databases, metadata capture and harmonization, statistical and network analyses, Cytoscape-compatible visualization, and optional scaling via cloud computing resources.