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Download sequences from BOLD Systems

Source: R/download.R
download_bold_db.Rd

lifecycle-experimental

Downloads reference sequences from BOLD Systems (Barcode of Life Data) for a given taxonomic group. Unlike other databases, BOLD does not provide a single pre-built reference FASTA — sequences are queried by taxon via the BOLD API.

Usage

download_bold_db(
  dest_dir = ".",
  taxon = NULL,
  marker = "COI-5P",
  tax_format = c("dada2", "sintax", "none"),
  verbose = TRUE
)

Arguments

dest_dir

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

taxon

(Character, required) Taxonomic name to query (e.g., "Fungi", "Arthropoda", "Mammalia").

marker

(Character, default "COI-5P") The barcode marker. Common values: "COI-5P", "ITS", "matK", "rbcL".

tax_format

(Character, default "dada2") Taxonomy format written into the FASTA headers, so the file can feed MiscMetabar::add_new_taxonomy_pq(). One of:

  • "dada2": unprefixed, positional ranks (>Phylum;Class;Order;Family;Genus;Species;).

  • "sintax": >processid;tax=p:Phylum,c:Class,....

  • "none": the raw BOLD sequence FASTA with processid|taxon|marker headers (no ranked taxonomy).

verbose

(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Details

This function uses the BOLD public API hosted at v3.boldsystems.org, which remains available after the main BOLD site's migration to v5. With tax_format = "none" it queries the sequence endpoint (FASTA). With "dada2"/"sintax" it queries the combined endpoint (TSV with the full ranked taxonomy), keeps the requested marker, and writes a taxonomy-headed FASTA (gaps removed). BOLD's taxonomy starts at phylum, so the dada2 output has no kingdom level.

For very large taxa the download may be slow or hit server limits; use narrower queries, or the BOLDconnectR package for the full v5 (BCDM) data model.

Please cite: Ratnasingham S & Hebert PDN (2007) BOLD: The Barcode of Life Data System. Molecular Ecology Notes 7:355-364. doi:10.1111/j.1471-8286.2007.01678.x

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# COI reference for a genus, dada2 taxonomy headers
download_bold_db(dest_dir = "databases", taxon = "Danaus")

# ITS sequences for an order, SINTAX headers
download_bold_db(
  dest_dir = "databases",
  taxon = "Agaricales",
  marker = "ITS",
  tax_format = "sintax"
)
} # }