[meta]
name = "prokka"
category = "metagenomics"
description = "Rapid prokaryotic genome annotation pipeline for bacteria, archaea, and viruses"
tags = ["annotation", "genome", "prokaryote", "bacteria", "gff", "genbank", "metagenomics", "assembly"]
author = "oxo-call built-in"
source_url = "https://github.com/tseemann/prokka"

[context]
concepts = [
    "Prokka annotates assembled prokaryotic genomes; input is a nucleotide FASTA (contigs/scaffolds).",
    "Use --outdir to specify output directory and --prefix for output file prefix.",
    "Prokka outputs: GFF3, GenBank, FASTA (proteins and CDS), TSV table, and text statistics.",
    "Use --kingdom to specify organism type: Bacteria (default), Archaea, Mitochondria, Viruses.",
    "Use --genus and --species for taxonomy-specific database searches (improves annotation).",
    "Use --cpus N for parallel processing; --gram to specify Gram stain for signal peptide prediction.",
    "For metagenome-assembled genomes (MAGs), use --metagenome flag for more permissive annotation.",
    "Use --proteins to add custom protein FASTA database for annotation (e.g., organism-specific proteins).",
]

pitfalls = [
    "Prokka requires contigs to be in multi-FASTA format — single sequences must be properly formatted.",
    "--outdir must be a new directory — Prokka will not overwrite existing output without --force.",
    "For repeat-heavy assemblies or metagenomes, use --metagenome to avoid missing fragmented features.",
    "Prokka uses a heuristic database search; custom --proteins databases greatly improve accuracy for specific taxa.",
    "Sequence IDs in the FASTA are used as scaffold names — ensure they are ≤20 characters for GenBank compatibility.",
    "--locustag sets the locus tag prefix for gene IDs; use a unique prefix per genome for multi-genome studies.",
]

[[examples]]
task = "annotate a bacterial genome assembly"
args = "--kingdom Bacteria --genus Escherichia --species coli --strain K12 --cpus 8 --outdir prokka_output --prefix ecoli_K12 assembly.fasta"
explanation = "--kingdom, --genus, --species improve annotation; --prefix names output files; --outdir output directory"

[[examples]]
task = "annotate a metagenome-assembled genome (MAG)"
args = "--metagenome --cpus 8 --outdir mag_annotation --prefix bin001 bin001_contigs.fasta"
explanation = "--metagenome mode for MAGs; increases sensitivity for fragmented genome annotation"

[[examples]]
task = "annotate archaea genome"
args = "--kingdom Archaea --cpus 8 --outdir archaea_output --prefix archaea_sample archaea_assembly.fasta"
explanation = "--kingdom Archaea switches annotation databases appropriate for archaea"

[[examples]]
task = "annotate genome with custom protein database for improved annotation"
args = "--kingdom Bacteria --proteins custom_proteins.faa --cpus 8 --outdir custom_annotation --prefix sample genome.fasta"
explanation = "--proteins adds custom protein FASTA for database-driven annotation; takes priority over defaults"

[[examples]]
task = "annotate genome and add specific locus tag prefix"
args = "--kingdom Bacteria --locustag MYORG --cpus 8 --outdir annotated --prefix genome_v1 assembly.fasta"
explanation = "--locustag sets locus tag prefix for gene names (e.g., MYORG_00001); important for GenBank submissions"
