MetaAMRSpotter: Automated workflow with shell scripting for uncovering hidden AMR hotspots from metagenomes v1

This protocol employs a novel, open-source automated pipeline scripted entirely in shell for analyzing metagenomic data from various samples. Designed to streamline the workflow, the pipeline integrates functionalities for pathogen identification, antimicrobial resistance (AMR) gene detection, and listing the probable antibiotics to which the genes are resistant. This user-friendly pipeline eliminates the need for manual tools installation and configuration, simplifying the analysis process. It directly analyzes raw sequencing reads, if there is presence of appropriate reference genomes and runs through the pipeline for each sample. This protocol runs nine tools together, with just one input given at the start of the program. Demonstrated using publicly available data on both a desktop Linux system and a high-performance computing cluster, the pipeline acknowledges potential variations arising from different software tools and versions, providing users the flexibility to modify them as needed. This approach offers a robust solution for metagenomic data analysis from varied samples, facilitating efficient and accurate detection and uncovering of hidden AMR hotspots.