Skip to contents

Download a Greengenes2 reference database

Source: R/download.R
download_greengenes2_db.Rd

lifecycle-experimental

Downloads the Greengenes2 16S rRNA database. By default, downloads the dada2-formatted training sets from Zenodo (maintained by Benjamin Callahan). Alternatively, downloads backbone sequences from the Greengenes2 FTP server.

Note that Greengenes2 uses d__ (domain) instead of k__ (kingdom) as the first rank prefix. Use tax_format = "greengenes2" with summarize_db() and list_ranks_db() for correct parsing.

Usage

download_greengenes2_db(
  dest_dir = ".",
  version = "2024.09",
  format = c("dada2", "dada2_species", "fasta"),
  tax_format = c("dada2", "sintax", "keep"),
  verbose = TRUE
)

Arguments

dest_dir

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

version

(Character, default "2024.09") Greengenes2 version in YYYY.MM format.

format

(Character, default "dada2") One of:

  • "dada2": dada2-formatted training set from Zenodo (recommended for dada2::assignTaxonomy()).

  • "dada2_species": species-level training set for dada2::assignTaxonomy() (includes species).

  • "fasta": plain FASTA sequences from the FTP server.

tax_format

(Character, default "dada2") How to write taxonomy in the headers of the "dada2"/"dada2_species" training set. The Greengenes2 trainset ships with d__/p__ rank prefixes, which dada2::assignTaxonomy() and MiscMetabar::add_new_taxonomy_pq() reject. One of:

  • "dada2": strip the prefixes to unprefixed, positional dada2 (>Bacteria;Pseudomonadota;...;).

  • "sintax": rewrite as >ID;tax=d:Bacteria,p:....

  • "keep": leave the original d__-prefixed headers untouched. Ignored for format = "fasta".

verbose

(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Details

The dada2-formatted files are maintained by Benjamin Callahan on Zenodo and are the same source as the SILVA dada2 training sets. See https://benjjneb.github.io/dada2/training.html for details.

The Greengenes2 trainset uses d__/p__ rank prefixes. By default (tax_format = "dada2") the prefixes are stripped so the file is directly usable by dada2::assignTaxonomy() and add_new_taxonomy_pq().

Please cite: McDonald D et al. (2024) Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology 42:715-718. doi:10.1038/s41587-023-01845-1

See also

format2dada2(), tax_prefixes()

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Download dada2-formatted Greengenes2
download_greengenes2_db(dest_dir = "databases")

# Download plain FASTA from FTP
download_greengenes2_db(dest_dir = "databases", format = "fasta")
} # }