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Genome Retrieval

Source: R/getGenome.R
getGenome.Rd

Main genome retrieval function for an organism of interest. By specifying the scientific name of an organism of interest the corresponding fasta-file storing the genome of the organism of interest can be downloaded and stored locally. Genome files can be retrieved from several databases. In addition, the genome summary statistics for the retrieved species is stored locally to provide users with insights regarding the genome assembly quality (see summary_genome for details). This is useful when comparing genomes with large difference in genome assembly qualities.

Usage

getGenome(
  db = "refseq",
  organism,
  reference = FALSE,
  release = NULL,
  gunzip = FALSE,
  path = file.path("_ncbi_downloads", "genomes"),
  assembly_type = "toplevel"
)

Arguments

db

a character string specifying the database from which the genome shall be retrieved:

  • db = "refseq"

  • db = "genbank"

  • db = "ensembl"

organism

there are three options to characterize an organism:

  • by scientific name: e.g. organism = "Homo sapiens"

  • by database specific accession identifier: e.g. organism = "GCF_000001405.37" (= NCBI RefSeq identifier for Homo sapiens)

  • by taxonomic identifier from NCBI Taxonomy: e.g. organism = "9606" (= taxid of Homo sapiens)

reference

a logical value indicating whether or not a genome shall be downloaded if it isn't marked in the database as either a reference genome or a representative genome.

release

a numeric, the database release version of ENSEMBL (db = "ensembl"). Default is release = NULL meaning that the most recent database version is used. release = 75 would for human would give the stable GRCh37 release in ensembl. Value must be > 46, since ensembl did not structure their data if the standard format before that.

gunzip

a logical value indicating whether or not files should be unzipped.

path

a character string specifying the location (a folder) in which the corresponding genome shall be stored. Default is path = file.path("_ncbi_downloads","genomes").

assembly_type

a character string specifying from which assembly type the genome shall be retrieved from (ensembl only, else this argument is ignored): Default is assembly_type = "toplevel"). This will give you all multi-chromosomes (copies of the same chromosome with small variations). As an example the toplevel fasta genome in human is over 70 GB uncompressed. To get primary assembly with 1 chromosome variant per chromosome: assembly_type = "primary_assembly"). As an example, the primary_assembly fasta genome in human is only a few GB uncompressed:

Value

File path to downloaded genome.

Details

Internally this function loads the the overview.txt file from NCBI:

refseq: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/

genbank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/

and creates a directory '_ncbi_downloads/genomes' to store the genome of interest as fasta file for future processing. In case the corresponding fasta file already exists within the '_ncbi_downloads/genomes' folder and is accessible within the workspace, no download process will be performed.

See also

getGenomeSet, getProteome, getCDS, getGFF, getRNA, getRepeatMasker, getAssemblyStats, summary_genome, meta.retrieval, meta.retrieval.all, read_genome

Author

Hajk-Georg Drost

Examples

if (FALSE) {

# download the genome of Arabidopsis thaliana from refseq
# and store the corresponding genome file in '_ncbi_downloads/genomes'
file_path <- getGenome( db       = "refseq",
             organism = "Arabidopsis thaliana",
             path = file.path("_ncbi_downloads","genomes"))

Ath_genome <- read_genome(file_path, format = "fasta")


# download the genome of Arabidopsis thaliana from genbank
# and store the corresponding genome file in '_ncbi_downloads/genomes'
file_path <- getGenome( db       = "genbank",
             organism = "Arabidopsis thaliana",
             path = file.path("_ncbi_downloads","genomes"))

Ath_genome <- read_genome(file_path, format = "fasta")
}