Download the MaarjAM reference database — download_marjaam

Downloads the MaarjAM database of arbuscular mycorrhizal fungi (AMF) virtual taxa (VT) sequences, maintained at the University of Tartu. The QIIME-formatted release (a zip bundling a FASTA and a taxonomy table) is used so that the resulting FASTA carries taxonomy in its headers, ready for MiscMetabar::add_new_taxonomy_pq().

Usage

download_marjaam_db(
  dest_dir = ".",
  dataset = c("SSU", "SSU_TYPE", "LSU", "full_ITS", "onlyITS"),
  tax_format = c("dada2", "sintax", "none"),
  url = NULL,
  verbose = TRUE
)

Arguments

dest_dir: (Character, default ".") Directory to save the downloaded file.
dataset: (Character, default "SSU") Which MaarjAM marker release to download. One of "SSU", "SSU_TYPE", "LSU", "full_ITS", "onlyITS".
tax_format: (Character, default "dada2") Taxonomy format written into the FASTA headers. One of "dada2", "sintax", or "none" (keep the QIIME accession_VTX... headers without taxonomy).
url: (Character) Direct download URL for the MaarjAM QIIME zip. If NULL (default), it is built from dataset. Override if the URL has changed.
verbose: (Logical, default TRUE) Print progress messages.

Value

The path to the downloaded FASTA file (invisibly).

Details

The download links are listed at https://maarjam.ut.ee/?action=bDownload. The QIIME zip contains *.qiime.fasta and *.qiime.txt (a tab-separated id k__Fungi;p__...;s__VTX... table); taxonomy is merged into the FASTA headers by matching sequence IDs.

Please cite: Opik M et al. (2010) The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188:223-241. doi:10.1111/j.1469-8137.2010.03334.x

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# SSU (18S) AMF database with dada2 taxonomy headers
download_marjaam_db(dest_dir = "databases")

# SINTAX-formatted headers
download_marjaam_db(dest_dir = "databases", tax_format = "sintax")
} # }