Mycobacterium abscessus Complex (MABC) Pangenomics

This repository contains an automated pangenomics and metabolic pipeline for analyzing 12 isolates of the Mycobacterium abscessus complex.

Directory Structure

• 01_FASTA/: Contains decompressed and formatted genome assemblies.
• 02_CONTIGS/: Individual .db databases for each isolate containing coding sequences and annotations.
• 03_PAN/: Holds the computed pangenome (MAb_Pan-PAN.db) and the merged genomes storage database (MAb-GENOMES.db).
• 04_METABOLISM/: Metabolic metrics, enrichment matrices, and the profile database.
• 05_ANI/: FastANI output matrices and Newick trees for genomic similarity.
• 06_MABC_PAN_images/: Example PNG images generated during the analysis, showing the pangenome and metabolic heatmaps.

Usage

To execute the entire pipeline from start to finish:

bash script.sh

Note: Ensure you have the Anvi'o 9 Conda environment properly configured and activated prior to running the pipeline.

Visualization

You can interactively visualize the results using these key Anvi'o tools:

• Pangenome Structure: anvi-display-pan -p 03_PAN/MAb_Pan-PAN.db -g MAb-GENOMES.db
• Metabolic Heatmap: anvi-interactive --manual -d 04_METABOLISM/MAb_Metabolic_Modules-module_pathwise_completeness-MATRIX.txt -p 04_METABOLISM/METABOLISM-PROFILE.db
• Single Isolate Pathway Maps: anvi-display-metabolism -c 02_CONTIGS/<isolate_name>.db