[meta]
name = "bakta"
category = "annotation"
description = "Fast and standardized annotation of bacterial genomes and plasmids in GFF3 and GenBank format"
tags = ["annotation", "bacteria", "genome", "gff", "genbank", "plasmid", "ncbi", "insdc"]
author = "oxo-call built-in"
source_url = "https://github.com/oschwengers/bakta"

[context]
concepts = [
    "Bakta is a modern prokaryotic annotation tool that produces INSDC/NCBI-compliant annotation files.",
    "Use --db to specify the Bakta database path (download with 'bakta_db download --output /path/to/db').",
    "Use -o for output directory; --prefix for output file prefix; --threads for parallelism.",
    "Bakta outputs: GFF3, GenBank/EMBL, TSV table, FAA, FNA, log files.",
    "Use --gram to specify Gram stain (+/-) for signal peptide prediction.",
    "Use --genus and --species for taxonomy-aware annotations.",
    "Bakta is recommended over Prokka for NCBI submissions due to better standard compliance.",
    "Use --compliant for INSDC-compliant sequence IDs (required for GenBank/EMBL submission).",
]

pitfalls = [
    "Bakta database must be downloaded before running — use 'bakta_db download' first.",
    "--db must point to the full database directory, not just a file within it.",
    "The output directory must not already exist — Bakta creates it fresh.",
    "For NCBI submission, always use --compliant and set --locus-tag.",
    "Bakta requires sequences ≥200 bp — very short contigs may not produce annotations.",
    "Without --gram, signal peptide prediction defaults to both orientations.",
]

[[examples]]
task = "annotate a bacterial genome with Bakta"
args = "--db /path/to/bakta_db/ --threads 8 --output annotation/ --prefix genome_annotation genome.fasta"
explanation = "--db database path; --threads 8; --output directory; --prefix file naming prefix"

[[examples]]
task = "annotate genome for NCBI submission"
args = "--db /path/to/bakta_db/ --compliant --locus-tag MYORG --genus Escherichia --species coli --threads 8 --output ncbi_annotation/ --prefix ecoli_K12 genome.fasta"
explanation = "--compliant INSDC-compliant format; --locus-tag gene name prefix; required for NCBI submission"

[[examples]]
task = "annotate plasmid sequence"
args = "--db /path/to/bakta_db/ --plasmid --threads 4 --output plasmid_annotation/ --prefix plasmid plasmid.fasta"
explanation = "--plasmid adjusts for circular plasmid topology"
