Prodigal

# 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.