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Download a MIDORI2 reference database

Source: R/download.R
download_midori2_db.Rd

lifecycle-experimental

Downloads the MIDORI2 reference database for eukaryotic mitochondrial genes (COI, 12S, 16S, Cytb, etc.). MIDORI2 provides pre-formatted FASTA files for multiple classifiers (dada2, SINTAX, RDP, BLAST).

Usage

download_midori2_db(
  dest_dir = ".",
  gene = "CO1",
  format = c("dada2", "dada2_species", "SINTAX", "RDP", "BLAST"),
  seq_type = c("UNIQ", "LONGEST"),
  url = NULL,
  verbose = TRUE
)

Arguments

dest_dir

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

gene

(Character, default "CO1") Mitochondrial gene marker. Common values: "CO1", "srRNA" (12S), "lrRNA" (16S), "Cytb".

format

(Character, default "dada2") One of "dada2", "dada2_species", "SINTAX", "RDP", or "BLAST".

seq_type

(Character, default "UNIQ") One of "UNIQ" (all unique haplotypes per species) or "LONGEST" (single longest sequence per species).

url

(Character) Direct download URL. If NULL (default), the function provides instructions and the download page URL.

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

MIDORI2 download URLs include a date-stamped directory path that changes with each GenBank release, making fully programmatic access fragile. Visit https://www.reference-midori.info/download.php to find the current download URL for your desired gene and format, then pass it via the url parameter.

Files are typically named following this pattern: MIDORI2_{TYPE}_NUC_SP_GB{VERSION}_{GENE}_{FORMAT}.fasta.gz

Please cite: Leray M et al. (2022) MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environmental DNA 4:894-907. doi:10.1002/edn3.303

See also

format2sintax(), format2dada2()

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Get instructions for downloading MIDORI2
download_midori2_db()

# Download with a specific URL
download_midori2_db(
  dest_dir = "databases",
  url = "https://reference-midori.info/download/Databases/..."
)
} # }