meta.retrieval.all {biomartr}R Documentation

Perform Meta-Genome Retrieval of all organisms in all kingdoms of life


Download genomes, proteomes, cds, gff, rna, or assembly stats files of individual species of all kingdoms of life.


meta.retrieval.all(db = "refseq", type = "genome", reference = FALSE)



a character string specifying the database from which the genome shall be retrieved:

  • db = "refseq"

  • db = "genbank"

  • db = "emsembl"

  • db = "ensemblgenomes"


type of sequences that shall be retrieved. Options are:

  • type = "genome" : for genome assembly retrieval; see also getGenome),

  • type = "proteome" : (for proteome retrieval; see also getProteome),

  • type = "cds" : (for coding sequence retrieval; see also getCDS),

  • type = "gff" : (for annotation file retrieval in gff format; see also getGFF),

  • type = "gtf" : (for annotation file retrieval in gtf format (only for ensembl and ensemblgenomes); see also getGTF),

  • type = "rna" : (for RNA file retrieval in fasta format; see also getRNA),

  • type = "rm" : (for Repeat Masker output file retrieval; see also getRepeatMasker),

  • type = "assemblystats" (for genome assembly quality stats file retrieval; see also getAssemblyStats).


a logical value indicating whether or not a genome shall be downloaded if it isn't marked in the database as either a reference genome or a representative genome. Options are:

  • reference = FALSE (Default): all organisms (reference, representative, and non-representative genomes) are downloaded.

  • reference = TRUE: organisms that are downloaded must be either a reference or representative genome. Thus, most genomes which are usually non-reference genomes will not be downloaded.


This function aims to perform bulk retrieval of all genomes of species for all kingdoms of life.


a character vector storing the file paths of the retrieved files.


Hajk-Georg Drost

See Also

Other meta_retrival: meta.retrieval()


## Not run: 
# download all genomes from refseq
meta.retrieval.all(db = "refseq", type = "genome")
# download all vertebrate genomes from genbank
meta.retrieval.all(db = "genbank", type = "genome")
# download all vertebrate genomes from ensemblgenomes
meta.retrieval.all(db = "genbank", type = "ensemblgenomes")

## End(Not run)

[Package biomartr version 1.0.7 Index]