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

DatabaseMySQLTSVEMFMAFXML
Pan_compara Multi-speciesMySQLTSVEMFXML
Metazoa Multi-speciesMySQLTSVEMFMAFXML
Ensembl MartMySQL

Single species data

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

SpeciesDNA (FASTA)cDNA (FASTA)CDS (FASTA)ncRNA (FASTA)Protein sequence (FASTA)Annotated sequence (EMBL)Annotated sequence (GenBank)Gene setsOther annotationsWhole databasesVariation (GVF)Variation (VCF)Variation (VEP)
YCaenorhabditis elegans (PRJNA13758)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YAnopheles gambiaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YDrosophila melanogasterFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YApis mellifera (DH4)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YOctopus bimaculoidesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Acanthaster planci (Crown-of-thorns starfish) - GCA_001949145.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Acropora millepora (Stony coral, JS-1) - GCA_013753865.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Actinia equina (AE1) - GCA_011057435.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Actinia tenebrosa (Australian red waratah sea anemone) - GCA_009602425.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Acyrthosiphon pisum (AL4f)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Adineta vagaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aedes aegypti (LVP_AGWG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Aedes albopictusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Agrilus planipennis (Emerald ash borer, EAB-ADULT) - GCA_000699045.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Amphibalanus amphitrite (Acorn barnacle, SeventyFive) - GCA_019059575.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Amphimedon queenslandicaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anneissia japonica (Sea lily, Jap-2015-1) - GCA_011630105.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles albimanusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles arabiensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles atroparvusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles atroparvus (EBRE) - GCA_914969975.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles christyiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles coluzziiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles coluzzii (Ngousso)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles culicifaciesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles darlingiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles dirusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles epiroticusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles farautiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles funestusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles maculatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles melasFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles merusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles minimusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles quadriannulatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles sinensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles sinensis (China)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles stephensiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles stephensi (Indian)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anoplophora glabripennis (ALB-LARVAE)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphidius gifuensis (Parasitoid wasp, YNYX2018) - GCA_014905175.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aplysia californica (California sea hare, F4 #8) - GCA_000002075.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ascaris suum (PRJNA62057)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Asterias rubens (European starfish) - GCA_902459465.3FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Athalia rosae (Coleseed sawfly, CS-ADULT) - GCA_000344095.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Atta cephalotesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bactrocera dorsalis (Oriental fruit fly, Punador) - GCA_000789215.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bactrocera latifrons (Solanum fruit fly, USDA-ARS-PBARC rearing strain) - GCA_001853355.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bactrocera tryoni (Queensland fruitfly, S06) - GCA_016617805.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Belgica antarcticaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (ASIAII-5)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA1-SG1 NG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA1-SG1 UG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA2 NG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA3 NG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (Uganda 1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Biomphalaria glabrataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Bombus impatiensFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bombus terrestrisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bombyx mori (p50T)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Branchiostoma lanceolatumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Brugia malayi (PRJNA10729)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis brenneri (PRJNA20035)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis briggsae (PRJNA10731)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis japonica (PRJNA12591)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis remanei (PRJNA53967)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Capitella teletaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Centruroides sculpturatus (CEXI.00-Female) - GCA_000671375.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ceratitis capitata (Mediterranean fruit fly) - GCA_000347755.4FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cimex lectularius (Harlan)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Clytia hemisphaerica (Z4C2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Copidosoma floridanum (CFLO.00-Male) - GCA_000648655.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cotesia glomerata (CgM1) - GCA_020080835.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Crassostrea gigas (Pacific oyster) - GCA_902806645.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Crassostrea virginica (RU13XGHG1-28) - GCA_002022765.4FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Culex quinquefasciatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Culex quinquefasciatus (JHB)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Culicoides sonorensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Danaus plexippus plexippus (F-2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Daphnia magnaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Daphnia magna (Fresh water planktonic, NIES) - GCA_020631705.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Daphnia pulexFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dendroctonus ponderosae (Mountain pine beetle) - GCA_000355655.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dendronephthya gigantea (DGI-Jeju-01) - GCA_004324835.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dermacentor silvarum (Dsil-2018)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dermatophagoides pteronyssinus (airmid) - GCA_001901225.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Diabrotica virgifera virgifera (Ped12-6-A-3) - GCA_003013835.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dimorphilus gyrociliatus (Segmented worms) - GCA_904063045.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dinothrombium tinctoriumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Diuraphis noxia (RWA2) - GCA_001186385.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila ananassae (TSC#14024-0371.13)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila erecta (TSC#14021-0224.01)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila grimshawi (TSC#15287-2541.00)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila mojavensis (TSC#15081-1352.22)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila persimilis (MSH-3)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila pseudoobscura pseudoobscura (MV2-25)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila sechellia (Rob3c)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila simulans (w501)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila virilis (TSC#15010-1051.87)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila willistoni (TSC#14030-0811.24)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila yakuba (Tai18E2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eurytemora affinis (Calanoid copepod, Atlantic clade) - GCA_000591075.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Exaiptasia diaphana (Sea anemone, CC7) - GCA_001417965.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Folsomia candida str. VU populationFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Gigantopelta aegis (Deep sea snail, Gae_Host) - GCA_016097555.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina austeniFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina brevipalpisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina fuscipes (IAEA_lab_2018)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina morsitansFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina pallidipesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina palpalisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Haemaphysalis longicornis (HaeL-2018)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Heliconius melpomeneFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Helobdella robustaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hermetia illucens (Black soldier fly) - GCA_905115235.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hofstenia miamiaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Homarus americanus (American lobster, GMGI-L3) - GCA_018991925.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hyalella azteca (Amphipod, HAZT.00-mixed) - GCA_000764305.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hyalomma asiaticum (Hyas-2018)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hydra vulgaris (Swiftwater hydra, 105) - GCA_000004095.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hymenolepis microstoma (PRJEB124)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hypsibius exemplaris (Water bear tardigrade, Z151) - GCA_002082055.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ixodes persulcatus (Iper-2018)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ixodes scapularisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Ixodes scapularis (ISE6)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ixodes scapularis (PalLabHiFi)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lepeophtheirus salmonisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leptinotarsa decemlineata (Colorado potato beetle, Imidocloprid resistant) - GCA_000500325.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leptotrombidium delienseFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Limulus polyphemus (Atlantic horseshoe crab) - GCA_000517525.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lingula anatinaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lingula anatina (Lamp shell (Brachiopod), Amm_Jpn) - GCA_001039355.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Loa loaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lottia giganteaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lucilia cuprinaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lutzomyia longipalpisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Lytechinus variegatus (Green sea urchin, NC3) - GCA_018143015.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Mayetiola destructorFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Megaselia scalarisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Melitaea cinxiaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Mercenaria mercenaria (Hard clam (quahog), YKG-2019) - GCA_014805675.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Metaseiulus occidentalis (Western predatory mite) - GCA_000255335.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Mizuhopecten yessoensis (Yesso scallop, PY_sf001) - GCA_002113885.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Mnemiopsis leidyiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Monomorium pharaonis (Pharaoh ant, MP-MQ-018) - GCA_013373865.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Musca domesticaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nasonia vitripennis (AsymCx)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Necator americanus (PRJNA72135)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nematostella vectensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Octopus bimaculoides (Octopus, UCB-OBI-ISO-001) - GCA_001194135.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Octopus sinensis (East Asian common octopus) - GCA_006345805.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Onchocerca volvulus (PRJEB513)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Onthophagus taurus (Dung beetle) - GCA_000648695.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ooceraea biroi (Clonal raider ant, clonal line C1) - GCA_003672135.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Orbicella faveolata (Mountainous star coral, FL) - GCA_002042975.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Orchesella cinctaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Orussus abietinus (Parasitic wood wasp, OABI.00-Male) - GCA_000612105.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Owenia fusiformis (Segmented worms) - GCA_903813345.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Parasteatoda tepidariorum (Goettingen) - GCA_000365465.3FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Patiria miniata (Bat star starfish, m_02_andy) - GCA_015706575.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pediculus humanusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Penaeus japonicus (Kuruma shrimp, Ginoza2017) - GCA_017312705.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Penaeus monodon (SGIC_2016) - GCA_015228065.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Penaeus vannamei (Pacific white shrimp) - GCA_003789085.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phlebotomus papatasiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Phlebotomus perniciosus (Murcia) - GCA_918844115.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pocillopora damicornis (RSMAS) - GCA_003704095.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pollicipes pollicipes (Goose neck barnacle, AB1234) - GCA_011947565.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pomacea canaliculata (SZHN2017) - GCA_003073045.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Portunus trituberculatus (Swimming crab, SZX2019) - GCA_017591435.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Priapulus caudatus (Penis worm) - GCA_000485595.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pristionchus pacificus (PRJNA12644)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Procambarus clarkii (Red swamp crayfish, Jiangsu) - GCA_020424385.2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Rhagoletis pomonella (Grant_MI) - GCA_013731165.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Rhipicephalus microplus (Rmic-2018)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Rhipicephalus sanguineus (Rsan-2018)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Rhodnius prolixusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Rhopalosiphum maidis (BTI-1) - GCA_003676215.3FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Saccoglossus kowalevskii (Acorn worm) - GCA_000003605.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Sarcoptes scabiei (SSS_KF_BRIS2020)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Schistosoma mansoni (PRJEA36577)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Sipha flava (LNK) - GCA_003268045.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Solenopsis invicta (M01_SB)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Stegodyphus mimosarumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Stomoxys calcitransFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Strigamia maritimaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Strongylocentrotus purpuratus (Spur 01)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Strongyloides ratti (PRJEB125)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Stylophora pistillata (CSM Monaco) - GCA_002571385.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Teleopsis dalmanni (2A)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tetranychus urticaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Thelohanellus kitaueiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tigriopus californicus (San Diego)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trialeurodes vaporariorum (IVF)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tribolium castaneumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trichinella spiralisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trichogramma pretiosum (Unisexual culture from Peru) - GCA_000599845.3FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trichoplax adhaerensFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trichuris muris (PRJEB126)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Varroa destructorFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Zootermopsis nevadensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--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/metazoa/.

The following files are provided:

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.