FTP Download

You can download via a browser from our FTP site, use a script, or even use rsync from the command line.

Globus

For rapid bulk download of files, the Ensembl FTP site is available as an end point in the Globus Online system. In order to access the data you need to sign up for an account with Globus, install the Globus Connect Personal software and setup a personal endpoint to download the data. The Ensembl data is hosted at the EMBL-EBI end point called “Shared EMBL-EBI public endpoint”. Data from the Ensembl FTP site can then be found under the "/gridftp/ensemblorg/pub" directory within the EMBL-EBI public end point.

API Code

If you do not have access to git, you can obtain our latest API code as a gzipped tarball:

Download complete API for this release

Note: the API version needs to be the same as the databases you are accessing, so please use git to obtain a previous version if querying older databases.

Database dumps

Entire databases can be downloaded from our FTP site in a variety of formats. Please be aware that some of these files can run to many gigabytes of data.

Looking for MySQL dumps to install databases locally? See our web installation instructions for full details.

Each directory on https://ftp.ebi.ac.uk/ensemblgenomes contains a README file, explaining the directory structure.

Multi-species data

Database	MySQL	TSV	EMF	MAF	XML
Pan_compara Multi-species	MySQL	TSV	EMF		XML
Plants Multi-species	MySQL	TSV	EMF	MAF	XML
Ensembl Mart	MySQL

Single species data

Popular species are listed first. You can customise this list via our home page.

	Species	DNA (FASTA)	cDNA (FASTA)	CDS (FASTA)	ncRNA (FASTA)	Protein sequence (FASTA)	Annotated sequence (EMBL)	Annotated sequence (GenBank)	Gene sets	Other annotations	Whole databases	Variation (GVF)	Variation (VCF)	Variation (VEP)
Y	Arabidopsis thaliana	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
Y	Oryza sativa Japonica Group	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
Y	Triticum aestivum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
Y	Hordeum vulgare	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
Y	Zea mays	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
Y	Physcomitrium patens	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Actinidia chinensis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Aegilops tauschii	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Amborella trichopoda	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Ananas comosus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Arabidopsis halleri	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Arabidopsis lyrata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Arabis alpina	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Asparagus officinalis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Avena sativa OT3098	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Avena sativa Sang	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Beta vulgaris	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Brachypodium distachyon	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Brassica juncea	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Brassica napus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Brassica oleracea	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Brassica rapa	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Brassica rapa R-o-18	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Cajanus cajan (pigeon pea) - GCA_000340665.1	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Camelina sativa	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Cannabis sativa female	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Capsicum annuum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Chara braunii	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Chenopodium quinoa	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Chlamydomonas reinhardtii	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Chondrus crispus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Citrullus lanatus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Citrus clementina	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Coffea canephora	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Corchorus capsularis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Corylus avellana	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Corymbia citriodora	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Cucumis melo	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Cucumis sativus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Cyanidioschyzon merolae	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Cynara cardunculus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Daucus carota	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Digitaria exilis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Dioscorea rotundata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Echinochloa crus-galli	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Eragrostis curvula	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Eragrostis tef	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Eucalyptus grandis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Eutrema salsugineum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Ficus carica	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Fraxinus excelsior	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Galdieria sulphuraria	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Glycine max	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Gossypium raimondii	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Helianthus annuus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Hordeum vulgare GoldenPromise	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Hordeum vulgare TRITEX	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Ipomoea triloba	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Juglans regia	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Kalanchoe fedtschenkoi	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Lactuca sativa	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Leersia perrieri	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Lolium perenne	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Lupinus angustifolius	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Malus domestica Golden	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Manihot esculenta	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Marchantia polymorpha	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Medicago truncatula	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Musa acuminata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Nicotiana attenuata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Nymphaea colorata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Olea europaea	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Olea europaea var. sylvestris	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza barthii	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza brachyantha	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza glaberrima	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Oryza glumipatula	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Oryza longistaminata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza meridionalis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza nivara	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza punctata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza rufipogon	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Oryza sativa Indica Group	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Ostreococcus lucimarinus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Panicum hallii FIL2	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Panicum hallii HAL2	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Papaver somniferum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Phaseolus vulgaris	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Pistacia vera	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Pisum sativum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Populus trichocarpa	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Prunus avium	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Prunus dulcis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Prunus persica	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Quercus lobata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Quercus suber	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Rosa chinensis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Saccharum spontaneum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Secale cereale	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Selaginella moellendorffii	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Sesamum indicum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Setaria italica	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Setaria viridis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Solanum lycopersicum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Solanum tuberosum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Solanum tuberosum RH89-039-16	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Sorghum bicolor	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Theobroma cacao Belizian Criollo B97-61/B2	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Theobroma cacao Matina 1-6	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Trifolium pratense	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Arinalrfor	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Cadenza	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Claire	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Jagger	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Julius	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Kariega	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Lancer	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Landmark	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Mace	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Norin61	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Paragon	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Robigus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Stanley	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Sy Mattis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum aestivum Weebill	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum dicoccoides	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum spelta	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Triticum turgidum	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP
	Triticum urartu	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Vigna angularis	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Vigna radiata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Vigna unguiculata	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	-	-	VEP
	Vitis vinifera	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV RDF JSON	MySQL	GVF	VCF	VEP

Metadata

Data files containing metadata for Ensembl Genomes from release 15 onwards can be found in the root directory or appropriate division directory of each release e.g. https://ftp.ebi.ac.uk/ensemblgenomes/pub/current/plants/.

The following files are provided:

species.txt (or e.g. species_EnsemblPlants.txt) - simple tab-separated file containing basic information about each genome
species_metadata.json (or e.g. species_metadata_EnsemblPlants.json) - full metadata about each genome in JSON format, including comparative analyses, sequence region names etc.
species_metadata.xml (or e.g. species_metadata_EnsemblPlants.xml) - full metadata about each genome in XML format, including comparative analyses, sequence region names etc.
uniprot_report.txt (or e.g. uniprot_report_EnsemblPlants.txt) - specialised tab-separated file containing information about mapping of genome to UniProtKB

To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed.

About the data

The following types of data dumps are available on the FTP site.

FASTA

FASTA sequence databases of Ensembl gene, transcript and protein model predictions. Since the FASTA format does not permit sequence annotation, these database files are mainly intended for use with local sequence similarity search algorithms. Each directory has a README file with a detailed description of the header line format and the file naming conventions.

DNA: Masked and unmasked genome sequences associated with the assembly (contigs, chromosomes etc.).; The header line in an FASTA dump files containing DNA sequence consists of the following attributes : coord_system:version:name:start:end:strand This coordinate-system string is used in the Ensembl API to retrieve slices with the SliceAdaptor.
CDS: Coding sequences for Ensembl or ab initio predicted genes.
cDNA: cDNA sequences for Ensembl or ab initio predicted genes.
Peptides: Protein sequences for Ensembl or ab initio predicted genes.
RNA: Non-coding RNA gene predictions.

Annotated sequence

Flat files allow more extensive sequence annotation by means of feature tables and contain thus the genome sequence as annotated by the automated Ensembl genome annotation pipeline. Each nucleotide sequence record in a flat file represents a 1Mb slice of the genome sequence. Flat files are broken into chunks of 1000 sequence records for easier downloading.

EMBL: Ensembl database dumps in EMBL nucleotide sequence database format
GenBank: Ensembl database dumps in GenBank nucleotide sequence database format

MySQL

All Ensembl MySQL databases are available in text format as are the SQL table definition files. These can be imported into any SQL database for a local installation of a mirror site. Generally, the FTP directory tree contains one directory per database. For more information about these databases and their Application Programming Interfaces (or APIs) see the API section.

GTF

Gene sets for each species. These files include annotations of both coding and non-coding genes. This file format is described here.

GFF3

GFF3 provides access to all annotated transcripts which make up an Ensembl gene set. This file format is described here.

EMF flatfile dumps (comparative data)

Alignments of resequencing data are available for several species as Ensembl Multi Format (EMF) flatfile dumps. The accompanying README file describes the file format.

Also, the same format is used to dump whole-genome multiple alignments as well as gene-based multiple alignments and phylogentic trees used to infer Ensembl orthologues and paralogues. These files are available in the ensembl_compara database which will be found in the mysql directory.

MAF (comparative data)

MAF files are provided for all pairwise alignments containing human (GRCh38), and all multiple alignments. The MAF file format is described here.

GVF (variation data)

GVF (Genome Variation Format) is a simple tab-delimited format derived from GFF3 for variation positions across the genome. There are GVF files for different types of variation data (e.g. somatic variants, structural variants etc). For more information see the "README" files in the GVF directory.

VCF (variation data)

VCF (Variant Call Format) is a text file format containing meta-information lines, a header line, and then data lines each containing information about a position in the genome. This file format can also contain genotype information on samples for each position. More details about the format and its specifications are available here.

VEP (variation data)

Compressed text files (called "cache files") used by the Variant Effect Predictor tool. More information about these files is available here.

BED format files (comparative data)

Constrained elements calculated using GERP are available in BED format. For more information see the accompanying README file.

BED format is a simple line-based format. The first 3 mandatory columns are:

chromosome name (may start with 'chr' for compliance with UCSC)
start position. This is a 0-based position
end position.

More information on the BED file format...

Tarball

The entire Ensembl API is gzipped and concatenated into a single TAR file. This is updated daily.

FTP Download

Globus

API Code

Database dumps

Multi-species data

Single species data

Metadata

About the data

About Us

Get help

Our sister sites

Follow us