Download a Diat.barcode reference database — download_diatbarcode

Downloads the Diat.barcode reference database for diatom rbcL barcoding. This is a curated database for diatom identification using the rbcL marker gene. The recommended access method is through the diatbarcode R package, which provides additional tools for working with the database.

Usage

download_diatbarcode_db(
  dest_dir = ".",
  format = c("dada2", "dada2_species"),
  url = NULL,
  verbose = TRUE
)

Arguments

dest_dir: (Character, default ".") Directory to save the downloaded file.
format: (Character, default "dada2") One of "dada2" or "dada2_species". Uses dada2-formatted files from the INRAE Dataverse.
url: (Character) Direct download URL. If NULL (default), the function provides instructions for using the diatbarcode R package.
verbose: (Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly), or a message with download instructions if no URL is provided.

Details

The Diat.barcode database is maintained by INRAE and hosted on Recherche Data Gouv. For more advanced access (metadata, full taxonomy tables, custom queries), consider using the diatbarcode R package directly:

diatbarcode::download_diatbarcode(
  path = "databases",
  flavor = "rbcl312_dada2_tax"
)

Please cite: Rimet F et al. (2019) Diat.barcode, an open-access curated barcode library for diatoms. Scientific Reports 9:15116. doi:10.1038/s41598-019-51500-6

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
download_diatbarcode_db(dest_dir = "databases")
} # }