Skip to contents

Download a SILVA reference database NR99 version

Source: R/download.R
download_silva_db.Rd

lifecycle-experimental

Downloads the SILVA ribosomal RNA database (16S/18S/23S/28S). By default, downloads the dada2-formatted training sets from the official arb-silva.de DADA2 release (available for both SSU and LSU). Can also produce a SINTAX-formatted database (converted locally from the dada2 trainset) or download the raw SILVA NR99 export.

For the PARC version (all sequences, not clustered like NR99), see dada2:::makeSpeciesFasta_Silva() on the manually downloaded FASTA file.

Usage

download_silva_db(
  dest_dir = ".",
  version = "138.2",
  target = c("SSU", "LSU"),
  format = c("dada2", "dada2_species", "sintax", "raw"),
  verbose = TRUE
)

Arguments

dest_dir

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

version

(Character, default "138.2") SILVA version number. Only the current SILVA release is hosted at the arb-silva DADA2 path used by the dada2/dada2_species/sintax formats.

target

(Character, default "SSU") One of "SSU" or "LSU".

format

(Character, default "dada2") One of:

  • "dada2": dada2-formatted toSpecies training set (NR99, recommended for dada2::assignTaxonomy()).

  • "dada2_species": species assignment file for dada2::addSpecies().

  • "sintax": VSEARCH/USEARCH SINTAX database, converted locally from the dada2 toSpecies trainset (7 ranks d,p,c,o,f,g,s). Sequence labels are synthetic (SILVA<version>_<target>_NNNNNN) because the dada2 trainset carries no accession. Written as a separate *_sintax.fasta.gz file.

  • "raw": raw SILVA NR99 FASTA with taxonomy from arb-silva.de.

verbose

(Logical, default TRUE) Print progress messages.

Value

The path to the resulting file (invisibly). For "sintax" this is the converted *_sintax.fasta.gz; the intermediate trainset is also kept in dest_dir.

Details

The dada2-formatted files are provided by arb-silva.de and are the recommended format for dada2::assignTaxonomy() and dada2::addSpecies(). See https://benjjneb.github.io/dada2/training.html for details.

SILVA data is free for academic use. Commercial use requires a license. See https://www.arb-silva.de/silva-license-information/.

Please cite: Quast C et al. (2013) The SILVA ribosomal RNA gene database project. Nucleic Acids Research 41:D590-D596. doi:10.1093/nar/gks1219

See also

format2dada2(), format2sintax()

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Download dada2-formatted SILVA for assignTaxonomy()
download_silva_db(dest_dir = "databases")

# Download species assignment file
download_silva_db(dest_dir = "databases", format = "dada2_species")

# Download a SINTAX database for SSU (converted from the dada2 trainset)
download_silva_db(dest_dir = "databases", format = "sintax")

# SINTAX database for LSU
download_silva_db(dest_dir = "databases", target = "LSU", format = "sintax")

# Download raw SILVA NR99 FASTA
download_silva_db(dest_dir = "databases", format = "raw")
} # }