Download RefSeq reference genome

downloadRefSeqGenome(
  organism,
  taxonomicGroup = NULL,
  genomeBuild = NULL,
  outputDir = "."
)

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). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").

outputDir

character(1). Output directory path.

Value

Invisible list.

Note

Updated 2021-02-17.

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

Examples

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