Metagenomic_analysis

Metagenomic analysis of the taxonomic composition and functional potential of microbial communities from different environmental samples.

Software Requirements:

• Operating System: Linux/Mac/Windows with WSL
• R (version 4.0+) with packages: phyloseq, vegan, ggplot2, dplyr
• Python (version 3.8+) with packages: pandas, numpy, matplotlib, seaborn
• FastQC for quality control
• Trimmomatic for read trimming
• Kraken2 for taxonomic classification
• QIIME2 (optional but recommended)

The metagenomic datasets from different environments:

1. Human gut microbiome (healthy vs. diseased)
2. Marine water samples (surface vs. deep water)
3. Soil samples (forest vs. agricultural)

Data Sources:

European Nucleotide Archive (ENA)

NCBI Sequence Read Archive (SRA)

MG-RAST database