Skip to contents

Download the LTPlus reference database

Source: R/download.R
download_ltplus_db.Rd

lifecycle-experimental

Downloads the LTPlus 16S rRNA gene reference FASTA for Bacteria and Archaea. LTPlus extends the All-Species Living Tree Project (LTP) type-strain collection with the best-quality non-type sequences selected from the SILVA non-redundant and GTDB databases, plus the highest-quality 16S sequences deposited at NCBI between 2019 and 2025. Sequences are clustered non-redundantly at a 98.7% identity threshold, yielding a compact database that covers most of the known prokaryotic genealogical diversity.

Usage

download_ltplus_db(
  dest_dir = ".",
  url = "https://biocom.uib.es/opucheck-backend/api/releases/02_26_06",
  tax_format = c("dada2", "sintax", "none"),
  csv_url = "https://biocom.uib.es/opucheck-backend/api/releases/02_26_02",
  to_dna = TRUE,
  verbose = TRUE
)

Arguments

dest_dir

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

url

(Character) Direct download URL for the LTPlus FASTA. Defaults to the February 2026 release served by the Marine Microbiology Group (IMEDEA, UIB-CSIC). Pass a different release URL to download another version (see Details).

tax_format

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

  • "dada2": unprefixed, semicolon-delimited ranks (>Bacteria;Pseudomonadota;...;).

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

  • "none": keep the original accession-only headers. Taxonomy is read from the companion CSV (see csv_url).

csv_url

(Character) URL of the LTPlus metadata CSV that maps each sequence accession to its full taxonomy. Defaults to the CSV of the February 2026 release. Only used when tax_format != "none".

to_dna

(Logical, default TRUE) Convert the downloaded RNA FASTA to DNA (transcribe U to T) and rewrite it as a standard FASTA. Set to FALSE to keep the original RNA file unchanged. Requires the Biostrings package.

verbose

(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Details

The file is the LTPlus 16S FASTA exported from the underlying curated alignment with gap columns removed ("compressed"), so the sequences are unaligned and vary in length (~140 MB total). It is served directly (no registration) from the LTP release backend; the file name is taken from the server's Content-Disposition header when available (e.g. ltplus_10_02_2026_compressed.fasta).

The released sequences are in the RNA alphabet (U rather than T) and the sequence lines contain whitespace. With to_dna = TRUE (default) the function transcribes U to T and rewrites a clean, whitespace-free DNA FASTA in place, ready for DNA-based classifiers such as dada2 or VSEARCH. With to_dna = FALSE the original RNA file is kept as-is.

The released FASTA headers carry only an accession (e.g. >LAJZ3046); the taxonomy lives in a companion CSV. With tax_format = "dada2" (default) or "sintax" the function downloads that CSV, maps each accession to its full LTPlus lineage, and rewrites the headers with taxonomy so the file is ready for MiscMetabar::add_new_taxonomy_pq(). Use tax_format = "none" to keep the accession-only headers.

The default url points to the current release file. To list available releases and files, see the Downloads section of https://bioinfo.uib.es/ltp/ or query https://biocom.uib.es/opucheck-backend/api/releases; each file has an id appended to .../api/releases/ to form its download URL. The ARB database, CSV and Newick tree files are also available there.

Please cite: Rosselló-Móra R et al. (2026) A pipeline for improved 16S rRNA gene-based phylogeny and diversity analyses of Bacteria and Archaea. Research Square. doi:10.21203/rs.3.rs-9370187/v1

See also

download_silva_db(), download_greengenes2_db(), download_ksgp_db()

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Download the current LTPlus 16S FASTA (DNA, dada2 taxonomy headers)
download_ltplus_db(dest_dir = "databases")

# SINTAX-formatted headers instead
download_ltplus_db(dest_dir = "databases", tax_format = "sintax")

# Keep the original RNA, accession-only FASTA without conversion
download_ltplus_db(dest_dir = "databases", to_dna = FALSE, tax_format = "none")
} # }