Download a UNITE reference database

Downloads the UNITE fungal ITS database for taxonomic assignment from the UNITE DOI repository (PlutoF/Zenodo). Provides both "dynamic" (including singletons) and "static" versions, for fungi or all eukaryotes.

UNITE general FASTA releases use the k__/p__ taxonomy format and are compatible with dada2, VSEARCH, and other classifiers after reformatting with format2dada2() or format2sintax().

Usage

download_unite_db(
  dest_dir = ".",
  type = c("dynamic", "static"),
  taxon_group = c("fungi", "eukaryotes"),
  version = "10.0",
  taxonomic_format = c("default", "sintax"),
  doi = NULL,
  verbose = TRUE
)

Arguments

dest_dir: (Character, default ".") Directory to save the downloaded file.
type: (Character, default "dynamic") One of "dynamic" or "static". Dynamic files include singletons. Only used when taxonomic_format = "default". Note: as of UNITE v10.0, separate static/dynamic archives are not available for taxon_group = "fungi"; both options download the same archive.
taxon_group: (Character, default "fungi") One of "fungi" or "eukaryotes".
version: (Character, default "10.0") UNITE version. Use "10.0" for the 2024 release.
taxonomic_format: (Character, default "default") One of "default" or "sintax". When "default", downloads the general FASTA release (.tgz archive with k__/p__ taxonomy). When "sintax", downloads a single FASTA file already formatted for VSEARCH SINTAX classification (with tax=d:... headers).
doi: (Character) If provided, overrides version-based URL construction with a direct DOI download. Useful for older or alternative releases.
verbose: (Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Details

When taxonomic_format = "default": since UNITE v10.0, the .tgz archive contains all clustering variants (dynamic, 97%, 99%) bundled together. After downloading, extract the archive and select the appropriate FASTA file.

When taxonomic_format = "sintax": the downloaded .gz file is a single FASTA with SINTAX-ready taxonomy headers. This file can be used directly with vsearch --sintax.

The S3 download URLs use opaque UUIDs that change between releases. If the automatic URL fails, visit https://unite.ut.ee/repository.php to find the current DOI and pass it via the doi parameter, or download manually.

Please cite UNITE: Abarenkov K et al. (2024) UNITE general FASTA release for Fungi. UNITE Community. doi:10.15156/BIO/2959336

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Download UNITE v10.0 default (general FASTA archive) for fungi
download_unite_db(dest_dir = "databases")

# Download UNITE v10.0 SINTAX-formatted for fungi
download_unite_db(dest_dir = "databases", taxonomic_format = "sintax")

# Download for all eukaryotes in SINTAX format
download_unite_db(
  dest_dir = "databases",
  taxon_group = "eukaryotes",
  taxonomic_format = "sintax"
)
} # }