A pipeline written in Snakemake to automatically generate pangenomes from metagenome assembled genomes (MAGs).
- 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).
- Unannotated MAGs (will be annotated with Bakta); OR
- GFF (with fasta)
Update config.yaml to specify workflow and directory paths.
Run snakemake (bash script for running on cluster using LSF):
bash submit_lsf.sh