blongpi - Bifidobacterium longum Comparative Genomics Pipeline

This project compares 28 B. longum MAGs between Control and Exposure infants.

Workflow:

1. Place MAG fasta files in data/mags/.
2. Run scripts/01.run_genomics.sh for annotation and pangenome.
3. Run scripts/02.search_functions.sh for targeted HMM searches.
4. Run scripts/03.analysis_viz.R for statistical enrichment and visualization.

Tasks Covered:

• Task 1: Pangenome enrichment (Exposure vs Control).
• Task 2: Phylogenomics & Clustering.
• Task 3: Metabolic potential (HMO/Adhesion).
• Task 4: Mobile Genetic Elements.
• Task 5: Correlation with ASV sharing metrics.