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

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, 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,
  fileformat = "fasta",
  simulate = TRUE
)

johnmcculloch/JAMS_BW documentation built on March 29, 2024, 7:56 p.m.