Table 1 MAGqual command line options and their usage
From: MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes
Command line option | Usage |
|---|---|
-a / --asm | Required: The location of the assembly in FASTA format used to generate the metagenome bins |
-b / --bins | Required: The location of the directory containing all the metagenome bins for quality assignation |
-p / --prefix | The prefix for the job. Default is MAGqual_YYYYMMDD |
-j / --jobs | Links to the Snakemake flag -j, the number of cores to use or if using the cluster option and the number of jobs to run at once. Default is 1 |
--cluster | Optional: The type of cluster to run MAGqual on a HPC system (available options: slurm), not to be used if running MAGqual locally |
--checkmdb | Optional: The location of a local install of the CheckM database |
--baktadb | Optional: The location of a local install of the Bakta database. Note: Must be v.5 or above |
-h / --help | Show help message |