Download an RDP reference database

Downloads the Ribosomal Database Project (RDP) 16S rRNA database. By default, downloads the dada2-formatted training sets from Zenodo (maintained by Benjamin Callahan).

Usage

download_rdp_db(
  dest_dir = ".",
  trainset = "19",
  format = c("dada2", "dada2_species"),
  verbose = TRUE
)

Arguments

dest_dir

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

trainset

(Character, default "19") RDP trainset version number.

format

(Character, default "dada2") One of:

"dada2": training set for dada2::assignTaxonomy().
"dada2_species": species assignment file for dada2::addSpecies().

verbose

(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Details

The dada2-formatted files are maintained by Benjamin Callahan on Zenodo. See https://benjjneb.github.io/dada2/training.html for details.

Please cite: Cole JR et al. (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research 42:D633-D642. doi:10.1093/nar/gkt1244

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Download RDP trainset 19 for assignTaxonomy()
download_rdp_db(dest_dir = "databases")

# Download species assignment file
download_rdp_db(dest_dir = "databases", format = "dada2_species")
} # }