Quickstart¶

1. Prepare your FASTA file
   Place your input file (e.g. in.fasta) in a data directory.

2. Configure the pipeline
   Edit config.yaml: ```yaml fasta: path/to/in.fasta scripts_dir: scripts

3. Run the pipeline
   Execute the Snakemake command to start the pipeline: bash snakemake --cores 1 or bash snakemake --cores 1 --config fasta=alt.fasta scripts_dir=myscripts This will run the pipeline using 1 core and the specified FASTA file and scripts directory.