Shotgun Metagenomics Profiler Comprehensive shotgun metagenomics analysis combining taxonomic classification, antimicrobial resistance gene detection, and functional pathway profiling from paired-end FASTQ files. What it does 1. Takes paired-end FASTQ files (R1, R2) or a single concatenated FASTQ as input 2. Runs Kraken2 taxonomic classification against a standard database (e.g., Standard-8, PlusPF) 3. Refines abundances with Bracken at species level (read re-estimation) 4. Detects antimicrobial resistance genes with RGI against the CARD database 5. Classifies detected ARGs by WHO critical pr…