mikado configure \ --list config_tab.txt \ --reference genome.fa \ --scoring scoring.yaml \ --copy-scoring mikado/scoring.yaml \ --out-dir /mikado \ /mikado/configuration.yaml mikado prepare \ -s \ -od /mikado \ --json-conf /mikado/configuration.yaml mikado serialise \ -od /mikado \ --json-conf /mikado/configuration.yaml mikado pick \ --configuration / mikado/configuration.yaml \ -od /mikado \ --subloci-out /mikado/mikado.subloci.gff3 \ --loci-out /mikado/mikado.loci.gff3