cheat sheet

Short and Long Options

Prodigal supports both long and short options. These four commands are all equivalent:

$ prodigal -i sequence.fna -o genes.gff -f gff
$ prodigal -isequence.fna -ogenes.gff -fgff
$ prodigal --input_file sequence.fna --output_file genes.gff --output_format gff
$ prodigal --input_file=sequence.fna --output_file=genes.gff --output_format=gff

Prodigal 2.x: Older versions of Prodigal only support short options, and there must be a space between each option and its parameter.

Help Output

You can obtain a complete list of options with the -h or --help option.

Usage:  prodigal [-a protein_file] [-c] [-d mrna_file]
                 [-e gap_mode] [-f out_format] [-g trans_table]
                 [-h] [-i input_file] [-n] [-o output_file]
                 [-p mode] [-q] [-s start_file] [-t train_file]
                 [-v] [-w summ_file]

Gene Modeling Parameters

  -p, --mode:           Specify mode (normal, train, or anon).
                          normal:   Single genome, any number of
                                    sequences.  (Default)
                          train:    Do only training.  Input
                                    should be multiple FASTA of
                                    one or more closely
                                    related genomes.
                          anon:     Anonymous sequences, analyze
                                    using preset training files,
                                    ideal for metagenomic data
                                    or single short sequences.
                          meta:     (Deprecated) Same as anon.
                          single:   (Deprecated) Same as normal.
  -g, --trans_table:    Specify a translation table to use.
                          auto: Tries 11 then 4 (Default)
                          11:   Standard Bacteria/Archaea
                          4:    Mycoplasma/Spiroplasma
                          #:    Other genetic codes 1-25
  -e, --gap_mode:       Specify gap-handling behavior.
                          0:    Partial genes run into gaps.
                                (Default)
                          1:    Genes cannot run into gaps.
                          2:    Do not treat N's as gaps.
  -c, --closed:         Closed ends.  Do not allow partial genes
                        at edges of sequence.
  -n, --force_nonsd:    Do not use the Shine-Dalgarno RBS finder
                        and instead force Prodigal to scan for
                        motifs.
  -t, --training_file:  Specify the training file location.  In
                        train mode, writes the training file.
                        In normal mode, reads the training file.
  -m:                   (Deprecated) Similar to '-e 1'.

Input/Output Parameters

  -i, --input_file:     Specify input file (default stdin).
  -o, --output_file:    Specify output file (default stdout).
  -a, --protein_file:   Specify protein translations file.
  -d, --mrna_file:      Specify nucleotide sequences file.
  -s, --start_file:     Specify complete starts file.
  -w, --summ_file:      Specify summary statistics file.
  -f, --output_format:  Specify output format.
                          gbk:  Genbank-like format (Default)
                          gff:  GFF format
                          sqn:  Sequin feature table format
                          sco:  Simple coordinate output
  -q, --quiet:          Run quietly (suppress logging output).

Other Parameters

  -h, --help:     Print help menu and exit.
  -v, --version:  Print version number and exit.