downloadRefseqGenome: Download RefSeq reference genome

In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations

Download RefSeq reference genome

Description

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.

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).

Note

Updated 2023-04-14.

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",
## > )

acidgenomics/AcidGenomes documentation built on Dec. 10, 2023, 10:35 p.m.