Genome annotation

Annotation adds taxonomic and functional context to recovered genomes. Aviary prepares the MAG inputs and coordinates external annotation tools; the reference databases and upstream software perform the classifications.

Basic usage

aviary annotate \
  --genome-fasta-directory recovery_run/bins/final_bins \
  --output annotation_run \
  --max-threads 16 \
  --n-cores 16

Use the literal option names shown by aviary annotate --help for the installed version; the CLI reference documents aliases and directory/extension controls.

Reference data matters

Taxonomic assignments depend on the configured GTDB data. Functional annotations depend on the configured EggNOG data. Record database releases alongside the Aviary version, and do not compare annotations produced from different releases as if the reference context were identical.

Outputs

Annotation products are written under annotation/, while raw taxonomic output may also appear under taxonomy/ depending on the selected targets. Consult the output reference and cite the upstream tools used by the run using the citation guide.