get_genomes_NCBI: get_genomes_NCBI(organisms = "bacteria", assembly_summary =...

In johnmcculloch/JAMS_BW: Just A Microbiology System

get_genomes_NCBI(organisms = "bacteria", assembly_summary = NULL, outputdir = NULL, assembly_accession = NULL, organism_name = NULL, infraspecific_name = NULL, taxid = NULL, species_taxid = NULL, asm_name = NULL, as_general_expression = FALSE, assembly_level = NULL, assembly_upto = NULL, bioproject = NULL, biosample = NULL, refseq_category_upto = NULL, ntop = NULL, nobs = TRUE, allow_assemblies_from_metagenomes = TRUE, fileformat = "fasta", simulate = TRUE)

Description

Downloads Genomes from NCBI GenBank based on matching criteria

Usage

get_genomes_NCBI(
  organisms = "bacteria",
  assembly_summary = NULL,
  outputdir = NULL,
  assembly_accession = NULL,
  organism_name = NULL,
  infraspecific_name = NULL,
  taxid = NULL,
  species_taxid = NULL,
  asm_name = NULL,
  as_general_expression = FALSE,
  assembly_level = NULL,
  assembly_upto = NULL,
  bioproject = NULL,
  biosample = NULL,
  refseq_category_upto = NULL,
  ntop = NULL,
  nobs = TRUE,
  allow_assemblies_from_metagenomes = TRUE,
  fileformat = "fasta",
  simulate = TRUE
)

johnmcculloch/JAMS_BW documentation built on Jan. 6, 2025, 5:14 a.m.