prodigal

name	prodigal
description	Use when predicting protein-coding genes in prokaryotic genomes or metagenomic sequences
disable-model-invocation	true
user-invocable	true

prodigal

Quick Start

• Command: prodigal -i input.fna -o output.gff -a proteins.faa
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/prodigal
• Version: Prodigal V2.6.3
• Full reference: See references/help.md

When To Use This Tool

• Predict protein-coding genes in bacterial or archaeal genomes.
• Annotate fragmented contigs or metagenomic assemblies with -p meta.
• Emit proteins, nucleotide CDS sequences, and GFF/GenBank/SCO annotations from the same run.
• Prefer prodigal for prokaryotic gene calling, not eukaryotic genome annotation.

Common Patterns

# 1) Standard prokaryotic genome annotation with proteins and GFF
prodigal \
  -i assembly.fna \
  -o genes.gff \
  -f gff \
  -a proteins.faa

# 2) Metagenome mode for fragmented contigs
prodigal \
  -i contigs.fna \
  -p meta \
  -o genes.gff \
  -a proteins.faa \
  -d cds.fna

# 3) Save and reuse a training file
prodigal \
  -i genome.fna \
  -t prodigal.trn \
  -o genes.gbk

Recommended Workflow

1. Start from a prokaryotic nucleotide assembly or contig set.
2. Choose -p single for a coherent isolate genome or -p meta for fragmented metagenomic data.
3. Always request proteins with -a, and often CDS sequences with -d, so downstream annotation has direct sequence inputs.
4. Review coordinates and translation outputs before chaining into functional annotation or comparative genomics.

Guardrails

• This is a prokaryotic gene finder; it is not appropriate for eukaryotic intron-rich genomes.
• The default translation table is 11; set -g explicitly for unusual genetic codes.
• Use -m if runs of N should break genes rather than being spanned.
• -v prints the version; --help and --version are not the right interface here.