armel001/Long-read-metagenomics-for-AMR-surveillance-in-hospital-and-community-wastewater-in-Guinea

Long-read metagenomics reveals a high burden of antimicrobial resistance, mobile genetic elements and bacterial diversity in hospital and community wastewater from Conakry, Guinea # Long-read metagenomics reveals a high burden of antimicrobial resistance, mobile genetic elements and bacterial diversity in hospital and community wastewater from Conakry, Guinea Statistical analysis and figure generation code for the manuscript (Gnimadi et al., in preparation; preprint: link). ## Overview This repository contains the downstream analysis performed on the outputs of two upstream pipelines — resistome/mobilome/taxonomic profiling (MetaSTREAM) and metagenome-assembled genome reconstruction (MagSTREAM). It does **not** reprocess raw sequencing reads; it consumes the summary matrices these pipelines produce and turns them into the statistics and figures reported in the manuscript. ## Pipelines used | Pipeline | Role in this study | Repository | |---|---|---| | **MetaSTREAM** | Quality control, taxonomic profiling (Kraken2/Bracken), resistome (RGI/CARD, assembly- and read-based), mobilome (mobileOG-db)| github.com | | **MagSTREAM** | Metagenome-assembled genome (MAG) reconstruction and quality assessment | github.com | See each pipeline's own README for installation, database setup, and full parameter documentation. Parameters specific to this study are recorded in `config/config.yaml` of each pipeline at the tagged version cited in the manuscript. ## Repository contents ``` notebooks/ Analysis notebooks (see mapping below) data/ Input matrices — outputs of MetaSTREAM / MagSTREAM figures/ Final exported figures ``` ## Notebook → manuscript mapping | Notebook | Produces | Input source | Kernel | |---|---|---|---| | `01_taxonomy_analysis.ipynb` | Figure 2, Table 1 | MetaSTREAM `results/taxonomy/`, `results/r_analysis/` | Python | | `02_resistome_analysis.ipynb` | Figure 3 | MetaSTREAM `results/r_analysis/rgi_bwt/` | Python | | `03_mobilome_analysis.ipynb` | Figure 4 | MetaSTREAM `results/r_analysis/mge/` | Python | | `04_cooccurence_analysis.ipynb` | Supplementary Table S (MAG-level ARG– …