MAG_pangenome_pipeline

A pipeline written in Snakemake to automatically generate pangenomes from metagenome assembled genomes (MAGs).

Dependencies:

• Snakemake (to get Snakemake to work with LSF click here)
• mmseqs2
• Bakta (if running annotation)
• Biopython
• BCBio
• Pandas

NOTE: Conda is used to call different environments and dependencies (see Snakemake file).

Input:

• Unannotated MAGs (will be annotated with Bakta); OR
• GFF (with fasta)

Quick start:

Update config.yaml to specify workflow and directory paths.

Run snakemake (bash script for running on cluster using LSF):

bash submit_lsf.sh