Download RefSeq reference genome

Download RefSeq reference genome

Usage

downloadRefseqGenome(
  organism,
  taxonomicGroup = NULL,
  genomeBuild = NULL,
  outputDir = getwd(),
  cache = FALSE
)

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

taxonomicGroup

character(1). Only applies to RefSeq. FTP server taxonomic group subdirectory path (e.g. "vertebrate_mammalian"). Defining this manually avoids having to query the FTP server.

genomeBuild

character(1). RefSeq genome build assembly name (e.g. "GCF_000001405.39_GRCh38.p12"). If set NULL, defauls to the most recent build available.

outputDir

character(1). Output directory path.

cache

logical(1). Cache URLs locally, using BiocFileCache internally.

Value

Invisible list.

Note

Updated 2023-04-14.

Stable release

The latest assembly defined under the "release/" subdirectory is not considered "stable" by the RefSeq team. It is considered good practice to use a genome build one version behind as a stable release (e.g. "GCF_000001405.38_GRCh38.p12" instead of current "GCF_000001405.39_GRCh38.p13" build).

See also

• Human Genome Resources at NCBI

• RefSeq Genomes FTP server

• Genomes Download (FTP) FAQ

• bcbio hg38 reference genome

• Heng Li: Which human reference genome to use?

• GRCh38 assembly for alignment pipelines

• UCSC hg38 bigZips

Examples

## This example is bandwidth intensive.
## > downloadRefseqGenome(
## >     organism = "Homo sapiens",
## >     taxonomicGroup = "vertebrate_mammalian",
## >     genomeBuild = "GCF_000001405.39_GRCh38.p12",
## > )