Mbaka-git/Embu-Diarrhea_study

Metagenomic analysis of stool samples from children with diarrhea in Embu, Kenya. # Embu-Diarrhea_study Metagenomic analysis of stool samples from children with diarrhea in Embu, Kenya. #Description This repository contains the complete bioinformatics analysis for a metagenomic study of 5 stool samples from children under the age of five years with diarrhea in Embu, Kenya. The study aims to characterize bacterial and viral pathogens using shotgun metagenomics and Kraken2/Bracken analysis #Samples - EMBA-14, EMBA-25, EMBA-43, EMBA-49, EMBA-54 #Methods 1. Quality control: `fastp` for read trimming 2. Taxonomic classification: Kraken2 + Bracken (species to phylum levels) 3. Bacterial analysis: Renormalized to 100% within bacteria 4. Viral analysis: Family-to-species level tracking 5. Coinfection analysis: Multiple pathogen detection per sample 6. Alpha diversity: Shannon, Simpson, Chao1, Observed species #Run analaysis scripts in order #initial data processing and quality control scripts 01_initial_qc.sh - FastQC initial quality assessment 02_trimming.sh - Read trimming with fastp 03_post_trim_qc.sh - Post-trimming quality control 04_quality_comparison.sh - Compare pre/post trimming quality #Taxonomy 01_kraken2.sh - Kraken2 classification 02_bracken_commands.sh - Bracken abundance re-estimation #Visualization Bar_plot_2026_Mar_10.R - heatmap_log_transformed Mar_11_2026.R Alpha_diversity_11_Mar_2026.R heatmap_log_transformed Mar_12_2026.R virus_12_mar_2026.R