Download the Eukaryome reference database — download_eukaryome

Downloads the Eukaryome database for eukaryotic organisms. Supports multiple markers (SSU 18S, ITS, LSU 28S) and output formats (general FASTA, dada2, mothur).

Usage

download_eukaryome_db(dest_dir = ".", url = NULL, verbose = TRUE)

Arguments

dest_dir: (Character, default ".") Directory to save the downloaded file.
url: (Character) Direct download URL for the Eukaryome file. Override if the URL has changed. If NULL (default), the function directs you to the Eukaryome download page.
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

Eukaryome does not provide a stable programmatic download API. Files are available at https://eukaryome.org/download/ in several formats:

General FASTA: https://eukaryome.org/generalfasta/
dada2 format: https://eukaryome.org/dada2/
mothur format: https://eukaryome.org/mothur/
SINTAX format: https://eukaryome.org/sintax/
QIIME2 format: https://eukaryome.org/qiime2/

Visit one of these pages, copy the direct download link, and pass it via the url parameter.

Please cite: Vasar M et al. (2024) Eukaryome: the rRNA gene reference database for identification of all eukaryotes. Database. doi:10.1093/database/baae043

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Download with a specific URL from the Eukaryome website
download_eukaryome_db(
  dest_dir = "databases",
  url = "https://eukaryome.org/files/eukaryome_v1.9_SSU_dada2.fasta.gz"
)
} # }