Metagenomics_V2

This repository contains a comprehensive pipeline for metagenomic analyses developed for our collaborative study, encompassing both taxonomic and functional aspects:

Features

Taxonomic Composition

• Visualisation: stacked barplots, heatmaps (ggplot2, pheatmap)
• Alpha Diversity: Chao1, Shannon, Simpson, Fisher indices (vegan)
• Beta Diversity: Bray-Curtis dissimilarityy, NMDS ordinations, PERMANOVA
• Differential Abundance: Maaslin2 linear models to identify taxa by metadata

Functional Profiling

• Functional Potential: Annotates and quantifies metabolic pathways and gene families (using tools like eggNOG-mapper)
• Visualisation: Pathway coverage and abundance barplots, KEGG pathway maps
• Comparative Functional Analysis: PERMANOVA or differential pathway abundance testing.

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Repository structure

data/     # input datasets (GTDB outputs, eggNOG-mapper outputs,metadata files)
docs/     # detailed markdown workflow notes, Mermaid crafted diagrams
figures/  # generated plots (barplots, heatmaps, NMDS, functional profiles)
scripst/  # bash, Python and R scripts for processing, analysis and visualisation

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Quickstart

Clone the repository:

git clone https://github.com/Dygasy/Metagenomics_V2.git
cd Metagenomics_V2

Create your environment (example if using miniconda):

conda env create -f environment.yml
conda activate metagenomics

Then run analyses, eg.:

Rscript scripts/taxonomic_analysis.R

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license

This project is licensed under the MIT license

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Citation

If you use this pipeline or adapt it in your research, please cite this repository (or the forthcoming manuscript).

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Contact

For questions, open an issue or contact Dygasy on Github.