Download a PR2 reference database

Downloads the PR2 protist ribosomal reference database from GitHub releases. PR2 provides 18S rRNA gene sequences for protists and other eukaryotes.

For more advanced access to PR2 data (e.g., full taxonomy tables, metadata, or custom queries), see the pr2database R package.

Usage

download_pr2_db(
  dest_dir = ".",
  version = NULL,
  format = c("dada2", "mothur", "UTAX", "sintax"),
  marker = c("SSU", "plastid"),
  verbose = TRUE
)

Arguments

dest_dir

(Character, default ".") Directory to save the downloaded file.

version

(Character) PR2 version number (e.g., "5.0.0"). If NULL (default), the latest release is fetched from GitHub.

format

(Character, default "dada2") One of "dada2", "mothur", "UTAX", or "sintax" (alias for "UTAX"). See Taxonomic ranks below: the "dada2" file keeps PR2's 9 ranks, whereas the "UTAX"/"sintax" file collapses them to 8 (Division and Subdivision are merged).

marker

(Character, default "SSU") One of "SSU" or "plastid".

verbose

(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Details

PR2 releases are hosted on GitHub at https://github.com/pr2database/pr2database/releases.

Taxonomic ranks

PR2 uses 9 taxonomic ranks. The "dada2" file keeps all nine as a positional, semicolon-delimited lineage (no rank prefixes); pass them to dada2::assignTaxonomy() (via MiscMetabar::add_new_taxonomy_pq() with method = "dada2") through taxLevels:

c("Domain", "Supergroup", "Division", "Subdivision", "Class", "Order", "Family", "Genus", "Species")

The "UTAX"/"sintax" file targets VSEARCH/USEARCH SINTAX and uses the 8 standard single-letter rank prefixes (k, d, p, c, o, f, g, s). To fit PR2's nine ranks onto them, PR2 merges Division and Subdivision into the p: rank (joined by -). The 9 → 8 mapping is:

PR2 rank (dada2)	SINTAX prefix (UTAX)
Domain	k:
Supergroup	d:
Division + Subdivision	p: (e.g. Alveolata-Dinoflagellata)
Class	c:
Order	o:
Family	f:
Genus	g:
Species	s:

Mind the per-method argument when calling MiscMetabar::add_new_taxonomy_pq():

• method = "dada2" (the "dada2" download) keeps all 9 ranks — pass the 9 names above as taxLevels (forwarded to dada2::assignTaxonomy()).

• method = "sintax" (the "sintax"/"UTAX" download) has 8 ranks — pass 8 names as taxa_ranks, e.g. c("Domain", "Supergroup", "Division_Subdivision", "Class", "Order", "Family", "Genus", "Species"). The dada2 taxLevels argument is ignored by the SINTAX path, so the default 7 ranks would be used and parsing the 8-rank output fails.

Please cite: Guillou L et al. (2013) The Protist Ribosomal Reference database (PR2). Nucleic Acids Research 41:D1108-D1113. doi:10.1093/nar/gks1160

See also

format2dada2(), format2sintax(), pr2database R package

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Download latest PR2 in dada2 format
download_pr2_db(dest_dir = "databases")

# Download specific version in UTAX format
download_pr2_db(dest_dir = "databases", version = "5.0.0", format = "UTAX")
} # }