salmonella_methylation_pipeline

SMP: A Salmonella enterica subsp. enterica Methylation Analysis Pipeline

How to operate the salmonella methylation pipeline:

1. Deposit sequencing data into the /sequencing_data directory
2. Modify serovar.design.tsv and setup.design.tsv in the \info directory
3. Deposit reference genomes and reference annotations
4. Run all scripts in \scripts in order, \scripts\bash_script_generator generates missing scripts