Download a taxonomic database and save it in UTAX format

Usage

load_taxdb(
  db_url,
  db_type = c("unite", "qiime_fasta", "qiime_qza"),
  db_file,
  db_tax_url = NULL,
  ...
)

db_url: Character vector with one or more file URLs; sequences from all URLs are combined into one final database.
db_type: Database type (character) (see details)
db_file: Output file (will be GZIPped FASTA, .fasta.gz)
db_tax_url: (optional) URL(s) pointing to file(s) containing the taxonomy for the sequences in the files at db_url (currently implemented for qiime_qza format)

Currently, three database types are implemented (more may follow):

"unite": UNITE ITS database (https://unite.ut.ee/repository.php): choose a dataset (e.g. all Eukaryotes), click on the file at Downloads and copy the actual file URL once the file starts downloading in the browser. The SH sequence set with a dynamic clustering threshold is chosen from the archive and imported.
"qiime_fasta": FASTA file with lineages in headers in the form <seqid> rank1__name; rank2__name; ... whereby rank1 and rank2 are one-letter codes such as k (for kingdom), g (for genus), etc. If only sequences are in the file, specify the URL of a tab-delimited file mapping sequence IDs to lineages. One example of database providing such files GTDB (e.g. here)
"qiime_qza": QIIME2 QZA format, which is essentially a ZIP file containing a qiime_fasta-formatted FASTA file, while another QZA file should contain the tab-delimited taxonomy (provide with db_tax_url).

This function may be expanded and made more flexible in the future