This repository contains the custom scripts used to perform metagenomic assembly, binning, quality assessment, and functional annotation as described in the associated manuscript. The workflow includes metagenome assembly, genome binning, gene prediction, genome quality evaluation, and downstream functional annotation of predicted genes against multiple reference databases. Functional annotation includes antibiotic resistance gene prediction, biosynthetic gene cluster identification, viral sequence detection, and database-based functional profiling. The scripts are provided as executable bash pipelines and are intended to ensure transparency and reproducibility of the analyses. All third-party software tools used in the workflow are publicly available and cited in the manuscript, along with their respective versions. Users should adapt input/output paths and database locations according to their local environment.