all `[filter]` Retrieves everthing Specified `[property]` Formal binomial and trinomial at or below species level `[property]` family `[rank]` Rank-based query taxonomy genome `[filter]` Taxa with a direct link to a genome sequence 2009/10/21:2020 `[date]` Date-bounded query mammalia `[subtree]` All taxa within the Mammalia extinct `[property]` Extinct organisms Terminal `[property]` Terminal nodes in the tree loprovencyclife `[filter]` Entries with LinkOut links to the Encyclopedia of Life

Source: R/fetch_sequences.R

fetch_genbank.Rd

Fetch sequences from genbank

fetch_genbank(
  x,
  database = "nuccore",
  marker = c("COI[GENE]", "CO1[GENE]", "COX1[GENE]"),
  output = "h",
  min_length = 1,
  max_length = 2000,
  subsample = FALSE,
  chunk_size = 100,
  db = NULL,
  multithread = FALSE,
  quiet = FALSE,
  progress = FALSE,
  retry_attempt = 3,
  retry_wait = 5
)

Arguments

x: A taxon name or vector of taxa to download sequences for
database: The database to download from. For NCBI GenBank this currently onlt accepts the arguments 'nuccore' or 'genbank' which is an alias for nuccore.
marker: The barcode marker used as a search term for the database. If this is set to "mitochondria" or "mitochondrion" it will download full mitochondrial genomes. If set to "genome" it will download entire genomes only.
output: The output format for the taxonomy in fasta headers. Options include "h" for full heirarchial taxonomy (Accession;Domain;Phylum;Class;Order;Family;Genus;Species), "binom" for just genus species binomials (Accession;Genus_species), "bold" for BOLD taxonomic ID only (Accession;BoldTaxID), "gb" for genbank taxonomic ID (Accession|GBTaxID), "gb-binom" which outputs genbank taxonomic ID's and Genus species binomials, translating BOLD taxonomic ID's to genbank in the process (Accession|GBTaxID;Genus_species) or "standard" which outputs the default format for each database. For bold this is sampleid|species name|markercode|genbankid
min_length: The minimum length of sequences to download
max_length: The maximum length of sequences to download
subsample: (Numeric) return a random subsample of sequences from the search.
chunk_size: Split up the query into chunks of this size to avoid overloading API servers. if left NULL, the default will be 300
db: a database file generated using taxreturn::get_ncbi_taxonomy(). Generated automatically if NULL.
multithread: Whether multithreading should be used, if TRUE the number of cores will be automatically detected, or provided a numeric vector to manually set the number of cores to use
quiet: Whether progress should be printed to the console.
progress: A logical, for whether or not to print a progress bar when multithread is true. Note, this will slow down processing.
retry_attempt: The number of query attempts in case of query failure due to poor internet connection.
retry_wait: How long to wait between query attempts.