Name:
Prokka 1.14.6 by Torsten Seemann <torsten.seemann@gmail.com>
Synopsis:
rapid bacterial genome annotation
Usage:
prokka [options] <contigs.fasta>
General:
--help This help
--version Print version and exit
--citation Print citation for referencing Prokka
--quiet No screen output (default OFF)
--debug Debug mode: keep all temporary files (default OFF)
Setup:
--dbdir [X] Prokka database root folders (default '/rome/software/miniconda3/envs/prokka/db')
--listdb List all configured databases
--setupdb Index all installed databases
--cleandb Remove all database indices
--depends List all software dependencies
Outputs:
--outdir [X] Output folder [auto] (default '')
--force Force overwriting existing output folder (default OFF)
--prefix [X] Filename output prefix [auto] (default '')
--addgenes Add 'gene' features for each 'CDS' feature (default OFF)
--addmrna Add 'mRNA' features for each 'CDS' feature (default OFF)
--locustag [X] Locus tag prefix [auto] (default '')
--increment [N] Locus tag counter increment (default '1')
--gffver [N] GFF version (default '3')
--compliant Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF)
--centre [X] Sequencing centre ID. (default '')
--accver [N] Version to put in Genbank file (default '1')
Organism details:
--genus [X] Genus name (default 'Genus')
--species [X] Species name (default 'species')
--strain [X] Strain name (default 'strain')
--plasmid [X] Plasmid name or identifier (default '')
Annotations:
--kingdom [X] Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria')
--gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0')
--prodigaltf [X] Prodigal training file (default '')
--gram [X] Gram: -/neg +/pos (default '')
--usegenus Use genus-specific BLAST databases (needs --genus) (default OFF)
--proteins [X] FASTA or GBK file to use as 1st priority (default '')
--hmms [X] Trusted HMM to first annotate from (default '')
--metagenome Improve gene predictions for highly fragmented genomes (default OFF)
--rawproduct Do not clean up /product annotation (default OFF)
--cdsrnaolap Allow [tr]RNA to overlap CDS (default OFF)
Matching:
--evalue [n.n] Similarity e-value cut-off (default '1e-09')
--coverage [n.n] Minimum coverage on query protein (default '80')
Computation:
--cpus [N] Number of CPUs to use [0=all] (default '8')
--fast Fast mode - only use basic BLASTP databases (default OFF)
--noanno For CDS just set /product="unannotated protein" (default OFF)
--mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')
--rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
--norrna Don't run rRNA search (default OFF)
--notrna Don't run tRNA search (default OFF)
--rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)