Current genome build

Fetch the current genome build (assembly) version from online resources.

Usage

currentEnsemblGenomeBuild(organism)

currentGencodeGenomeBuild(organism)

currentRefseqGenomeBuild(organism, taxonomicGroup = NULL)

currentUcscGenomeBuild(organism)

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.

Value

character(1). Genome assembly build version.

Note

Updated 2023-10-04.

See also

• Ensembl REST API.

• UCSC REST API.

• RefSeq genomes.

Examples

## Ensembl.
try({
    currentEnsemblGenomeBuild("Homo sapiens")
    currentEnsemblGenomeBuild("Mus musculus")
})
#> [1] "GRCm39"

## GENCODE.
try({
    currentGencodeGenomeBuild("Homo sapiens")
    currentGencodeGenomeBuild("Mus musculus")
})
#> [1] "GRCm39"

## RefSeq.
try({
    currentRefseqGenomeBuild(
        organism = "Homo sapiens",
        taxonomicGroup = "vertebrate_mammalian"
    )
    currentRefseqGenomeBuild(
        organism = "Mus musculus",
        taxonomicGroup = "vertebrate_mammalian"
    )
})
#> [1] "GCF_000001635.27_GRCm39"

## UCSC.
try({
    currentUcscGenomeBuild("Homo sapiens")
    currentUcscGenomeBuild("Mus musculus")
})
#> [1] "mm39"