sraX

sraX performs resistome analysis by detecting and annotating antibiotic resistance genes (ARGs) and validating resistance-associated mutations from assembled FASTA sequences to characterize resistomes and their genomic context.

Key Features:

• Automated pipeline: Executes a complete resistome analysis workflow on assembled FASTA sequences.
• Parallel genome analysis: Processes hundreds of bacterial genomes in parallel to detect and annotate putative resistance determinants.
• Genomic context analysis: Analyzes the arrangement and genomic context of ARGs to provide locus-level insights.
• Mutation validation: Validates known resistance-conferring mutations reported in reference studies.
• Drug-class and loci proportion profiling: Illustrates affected drug classes and proportions of different types of mutated loci.
• Integrated HTML results: Produces a single hyperlinked HTML file that integrates results for navigable presentation.

Scientific Applications:

• Resistome profiling: Generates detailed ARG inventories and profiles across samples.
• AMR pattern analysis: Discerns complex antimicrobial resistance patterns across datasets.
• Mechanism characterization: Supports identification and characterization of resistance mechanisms through mutation validation and genomic context.
• Comparative and epidemiological surveillance: Compares resistome diversity across samples and aids tracking of resistant strains.
• Public health insight: Summarizes resistome data to inform strategies addressing antimicrobial resistance.

Methodology:

Reads assembled FASTA sequence files, detects ARGs, annotates them within genomic context, validates known resistance mutations, and generates integrated HTML reports including illustrations of drug classes and loci proportions.