Download RefSeq reference genome

Download RefSeq reference genome

Usage

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

analysisSet

logical(1). Download the NCBI "no-alt analysis set" FASTA alongside the standard genome. This ALT-contig-free FASTA is recommended for aligners such as STAR that do not natively handle ALT contigs. Currently supported for GRCh38 and GRCm39. Defaults to FALSE.

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

• GenBank annotating genomes with GFF3 or GTF files

• db_xrefs

• 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",
## > )