pku-embl/metagenomics-skills/bakta

Bakta

Upstream: Bakta

Citation

Schwengers, O. et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb. Genom. 7, 000685 (2021). https://doi.org/10.1099/mgen.0.000685

See also docs/references.md.

Analytical thinking

Bakta provides rapid, standardized bacterial genome annotation with alignment-free sequence identification — preferred substrate for many new studies over Prokka when the Bakta DB is available.

Use on QC-filtered MAGs/genomes before antismash, dram, rgi, defensefinder. Not a substitute for catalogue-scale prodigal+clustering.

How to run

set -Eeuo pipefail
id="${1:?usage: annotate-bakta.sh GENOME_ID GENOME_FASTA DB_DIR OUTPUT_DIR}"
genome="${2:?usage: annotate-bakta.sh GENOME_ID GENOME_FASTA DB_DIR OUTPUT_DIR}"
db="${3:?usage: annotate-bakta.sh GENOME_ID GENOME_FASTA DB_DIR OUTPUT_DIR}"
out="${4:?usage: annotate-bakta.sh GENOME_ID GENOME_FASTA DB_DIR OUTPUT_DIR}"
threads="${THREADS:-8}"
[[ "$id" =~ ^[A-Za-z0-9][A-Za-z0-9._-]*$ ]] || exit 2
test -s "$genome" && test -d "$db" || exit 2
log_dir="${out}.logs"
test ! -e "$out" && test ! -e "$log_dir" || {
  echo "use new output and log paths" >&2; exit 2;
}
mkdir -p "$(dirname "$out")" "$log_dir"
 
bakta --db "$db" --threads "$threads" --output "$out" --prefix "$id" \
  "$genome" \
  >"$log_dir/bakta.stdout.log" 2>"$log_dir/bakta.stderr.log"

Key parameters

Decision tree

Genome annotation substrate?
├─ Bacterial MAG/isolate, modern default → bakta
├─ Minimal classic pipeline → prokka
└─ Mining next → bakta/prokka → microbial-mining tools

Validation, recovery, and provenance

Require non-empty JSON, GFF3, GenBank, nucleotide, and protein outputs expected for the pinned release. Reconcile input replicons/contigs, feature counts, translation table, locus tags, pseudogene/partial-call rates, and warnings; inspect anomalous coding density or rRNA/tRNA absence against MAG completeness. Downstream mining must consume outputs from the exact same annotation run.

Use a fresh output after changing genome, database, taxonomy hints, or release. Record Bakta and dependency versions, database type/version/checksum, input and output checksums, translation/replicon settings, command, logs, and feature summary. Annotation is database-supported prediction, not experimental function.

Related skills

prokka · prodigal · antismash · dram · rgi · defensefinder · mag-qc · microbial-mining · tool-selection