engkinandatama/AMR-gene-mobility

A reproducible end-to-end bioinformatics pipeline for comparative analysis of AMR gene–mobile genetic element associations across human gut metagenomes from Europe, Asia, and Africa. # AMR-MGE Co-localization Pipeline > **A reproducible end-to-end bioinformatics pipeline for comparative analysis of AMR gene–mobile genetic element associations across metagenomes from different study cohorts or geographic populations.** --- ## Overview This repository provides a reproducible, end-to-end framework to analyze whether antimicrobial resistance (AMR) gene–mobile genetic element (MGE) associations and co-localization patterns differ across populations, treatment groups, or geographic regions. It resolves both the *what* (AMR gene diversity/abundance) and the *how* (mechanistic linkage via plasmids, integrons, and insertion sequences/transposons). ### Research Questions Addressed This pipeline is designed to address key ecological and biological questions regarding resistome mobility, such as: 1. Do AMR gene diversity and abundance differ significantly across different study cohorts or populations? 2. Which MGE types (plasmid, integron, insertion sequence/transposon) predominantly carry AMR genes in each cohort? 3. Do AMR class–MGE type co-localization patterns differ across cohorts, suggesting distinct horizontal gene transfer (HGT) routes? --- ## Pipeline Architecture ``` INPUT: sample_map.csv │ ┌───────────────────────────────┴───────────────────────────────┐ │ snakemake assembly │ │ ================== │ │ 1. Download Raw Reads (sra-tools: prefetch + fasterq-dump) │ │ 2. Quality Control (fastp: adapter/quality filtering) │ │ 3. Host Depletion (Bowtie2 vs hg38: remove human reads) │ │ 4. Metagenome Assembly (MEGAHIT: contig generation) │ └───────────────────────────────┬───────────────────────────────┘ ▼ results/{run_id}/data/contigs/ │ ┌───────────────────────────────┴───────────────────────────────┐ │ snakemake annotation_aggregation │ │ ================================ …