pku-embl/metagenomics-skills/barrnap

Barrnap

Upstream: Barrnap

Citation

Seemann, T. Barrnap: BAsic Rapid Ribosomal RNA Predictor. https://github.com/tseemann/barrnap

See also docs/references.md.

Analytical thinking

Quick rRNA loci on MAGs/isolates for QC (16S presence) and annotation. Pair with GTDB-Tk / Prokka workflows.

How to run

Select the kingdom from independent taxonomy evidence; do not assume bacteria for every MAG.

set -Eeuo pipefail
id="${1:?usage: run-barrnap.sh GENOME_ID GENOME_FASTA OUTPUT_DIR}"
genome="${2:?usage: run-barrnap.sh GENOME_ID GENOME_FASTA OUTPUT_DIR}"
out="${3:?usage: run-barrnap.sh GENOME_ID GENOME_FASTA OUTPUT_DIR}"
kingdom="${BARRNAP_KINGDOM:-bac}"
threads="${THREADS:-4}"
[[ "$id" =~ ^[A-Za-z0-9][A-Za-z0-9._-]*$ ]] || exit 2
case "$kingdom" in bac|arc|euk|mito) ;; *) exit 2 ;; esac
test -s "$genome" || exit 2
test ! -e "$out" || { echo "use a new output directory: $out" >&2; exit 2; }
mkdir -p "$out"
 
barrnap --kingdom "$kingdom" --threads "$threads" "$genome" \
  >"$out/${id}.rrna.gff" 2>"$out/${id}.barrnap.stderr.log"

Key parameters

Decision notes

• Stage: function (rRNA prediction)
• Prefer as a quick rRNA check on genomes/MAGs; not a substitute for full annotation (bakta/prokka)

Validation, recovery, and provenance

A valid run may have no complete rRNA call, but the GFF and completed log must exist. Check sequence IDs/coordinates, partial flags, overlapping calls, expected 5S/16S/23S patterns, kingdom setting, and assembly-edge truncation. Absence of 16S in a fragmented MAG is not proof that the organism lacks the gene.

Record Barrnap/HMM database version, genome checksum, kingdom, command, logs, GFF checksum, and parsed feature summary. Rerun changed settings under a fresh path and keep rRNA evidence separate from whole-genome taxonomy.

Related skills

prokka · gtdbtk · checkm2 · tool-selection · metagenomics-workflow