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
Single species data
Popular species are listed first. You can customise this list via our home page .
Y Caenorhabditis elegans (PRJNA13758) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Y Anopheles gambiae FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Y Drosophila melanogaster FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Y Apis mellifera (DH4) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Y FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Y Octopus bimaculoides FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Acanthaster planci (Crown-of-thorns starfish) - GCA_001949145.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Acromyrmex echinatior (Panamanian leaf-cutter ant) - GCA_000204515.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Acropora millepora (Stony coral, JS-1) - GCA_013753865.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Actinia equina (AE1) - GCA_011057435.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Actinia tenebrosa (Australian red waratah sea anemone) - GCA_009602425.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Acyrthosiphon pisum (AL4f) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Adineta vaga FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Aedes aegypti (LVP_AGWG) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Aedes albopictus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Agrilus planipennis (Emerald ash borer, EAB-ADULT) - GCA_000699045.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Amphibalanus amphitrite (Acorn barnacle, SeventyFive) - GCA_019059575.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Amphimedon queenslandica FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anneissia japonica (Sea lily, Jap-2015-1) - GCA_011630105.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles albimanus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles arabiensis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles atroparvus (EBRE) - GCA_914969975.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles christyi FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles coluzzii FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles coluzzii (Ngousso) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles culicifacies FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles darlingi FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles dirus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles epiroticus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles farauti FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles funestus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles maculatus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles melas FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles merus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles minimus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles quadriannulatus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles sinensis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles sinensis (China) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Anopheles stephensi FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anopheles stephensi (Indian) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Anoplophora glabripennis (ALB-LARVAE) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Aphidius gifuensis (Parasitoid wasp, YNYX2018) - GCA_014905175.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Apis dorsata (Giant honeybee) - GCA_000469605.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Apis florea (Dwarf honeybee) - GCA_000184785.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Aplysia californica (California sea hare, F4 #8) - GCA_000002075.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Ascaris suum (PRJNA62057) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Asterias rubens (European starfish) - GCA_902459465.3 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Athalia rosae (Coleseed sawfly, CS-ADULT) - GCA_000344095.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Atta cephalotes FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bactrocera dorsalis (Oriental fruit fly, Punador) - GCA_000789215.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bactrocera latifrons (Solanum fruit fly, USDA-ARS-PBARC rearing strain) - GCA_001853355.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bactrocera tryoni (Queensland fruitfly, S06) - GCA_016617805.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Belgica antarctica FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bemisia tabaci (ASIAII-5) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bemisia tabaci (SSA1-SG1 NG) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bemisia tabaci (SSA1-SG1 UG) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bemisia tabaci (SSA2 NG) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bemisia tabaci (SSA3 NG) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bemisia tabaci (Uganda 1) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Biomphalaria glabrata FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Bombus impatiens FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bombus terrestris FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bombyx mandarina (Wild silkworm, Bman2017) - GCA_003987935.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Bombyx mori (p50T) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Branchiostoma lanceolatum FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Brugia malayi (PRJNA10729) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Caenorhabditis brenneri (PRJNA20035) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Caenorhabditis briggsae (PRJNA10731) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Caenorhabditis japonica (PRJNA12591) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Caenorhabditis remanei (PRJNA53967) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Camponotus floridanus (Florida carpenter ant, SB8) - GCA_003227725.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Capitella teleta FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Centruroides sculpturatus (CEXI.00-Female) - GCA_000671375.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Ceratitis capitata (Mediterranean fruit fly) - GCA_000347755.4 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Cimex lectularius (Harlan) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Clytia hemisphaerica (Z4C2) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Copidosoma floridanum (CFLO.00-Male) - GCA_000648655.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Cotesia glomerata (CgM1) - GCA_020080835.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Crassostrea gigas (Pacific oyster) - GCA_902806645.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Crassostrea virginica (RU13XGHG1-28) - GCA_002022765.4 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Culex quinquefasciatus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Culex quinquefasciatus (JHB) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Culicoides sonorensis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Danaus plexippus plexippus (F-2) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Daphnia magna (Fresh water planktonic, NIES) - GCA_020631705.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Daphnia pulex FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Daphnia pulex (Common water flea, KAP4) - GCA_021134715.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Daphnia pulicaria (Water flea, SC F1-1A) - GCA_021234035.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Dendroctonus ponderosae (Mountain pine beetle) - GCA_000355655.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Dendronephthya gigantea (DGI-Jeju-01) - GCA_004324835.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Dermacentor silvarum (Dsil-2018) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Dermatophagoides pteronyssinus (airmid) - GCA_001901225.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Diabrotica virgifera virgifera (Ped12-6-A-3) - GCA_003013835.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Dimorphilus gyrociliatus (Segmented worms) - GCA_904063045.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Dinothrombium tinctorium FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Diuraphis noxia (RWA2) - GCA_001186385.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila ananassae (TSC#14024-0371.13) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila erecta (TSC#14021-0224.01) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila grimshawi (TSC#15287-2541.00) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila mojavensis (TSC#15081-1352.22) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila persimilis (MSH-3) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila pseudoobscura pseudoobscura (MV2-25) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila sechellia (Rob3c) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila simulans (w501) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila virilis (TSC#15010-1051.87) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila willistoni (TSC#14030-0811.24) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Drosophila yakuba (Tai18E2) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Dufourea novaeangliae (Bee, 0120121106) - GCA_001272555.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Echinococcus granulosus (Dog tapeworm) - GCA_000524195.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Eufriesea mexicana (Bee, 0111107269) - GCA_001483705.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Eurytemora affinis (Calanoid copepod, Atlantic clade) - GCA_000591075.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Exaiptasia diaphana (Sea anemone, CC7) - GCA_001417965.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Folsomia candida str. VU population FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Galendromus occidentalis (Western predatory mite) - GCA_000255335.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Gigantopelta aegis (Deep sea snail, Gae_Host) - GCA_016097555.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Glossina austeni FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Glossina brevipalpis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Glossina fuscipes (IAEA_lab_2018) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Glossina morsitans FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Glossina pallidipes FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Glossina palpalis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Habropoda laboriosa (Southeastern blueberry bee, 0110345459) - GCA_001263275.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Haemaphysalis longicornis (HaeL-2018) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Haliotis rubra (Blacklip abalone, DU_JTF1) - GCA_003918875.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Haliotis rufescens (Red abalone, VD_foot) - GCA_023055435.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Harpegnathos saltator (Indian jumping ant, DR-91) - GCA_003227715.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Heliconius melpomene FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Helobdella robusta FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hermetia illucens (Black soldier fly) - GCA_905115235.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hofstenia miamia FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Homarus americanus (American lobster, GMGI-L3) - GCA_018991925.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hyalella azteca (Amphipod, HAZT.00-mixed) - GCA_000764305.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hyalomma asiaticum (Hyas-2018) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hydra vulgaris (Swiftwater hydra, 105) - GCA_000004095.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hydra vulgaris (Swiftwater hydra, 105) - GCA_022113875.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hymenolepis microstoma (PRJEB124) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Hypsibius exemplaris (Water bear tardigrade, Z151) - GCA_002082055.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Ixodes persulcatus (Iper-2018) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Ixodes scapularis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Ixodes scapularis (ISE6) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Ixodes scapularis (PalLabHiFi) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Lepeophtheirus salmonis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Lepeophtheirus salmonis (Salmon louse, Lsal2020) - GCA_016086655.3 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Leptinotarsa decemlineata (Colorado potato beetle, Imidocloprid resistant) - GCA_000500325.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Leptotrombidium deliense FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Limulus polyphemus (Atlantic horseshoe crab) - GCA_000517525.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Linepithema humile (Argentine ant) - GCA_000217595.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Lingula anatina FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Lingula anatina (Lamp shell (Brachiopod), Amm_Jpn) - GCA_001039355.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Loa loa FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Lottia gigantea FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Lucilia cuprina FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Lutzomyia longipalpis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Lytechinus variegatus (Green sea urchin, NC3) - GCA_018143015.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Mayetiola destructor FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Megachile rotundata (Alfalfa leafcutting bee) - GCA_000220905.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Megaselia scalaris FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Melitaea cinxia FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Mercenaria mercenaria (Hard clam (quahog), YKG-2019) - GCA_014805675.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Mizuhopecten yessoensis (Yesso scallop, PY_sf001) - GCA_002113885.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Mnemiopsis leidyi FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Monomorium pharaonis (Pharaoh ant, MP-MQ-018) - GCA_013373865.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Musca domestica FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Nasonia vitripennis (AsymCx) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Necator americanus (PRJNA72135) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Nematostella vectensis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Octopus bimaculoides (Octopus, UCB-OBI-ISO-001) - GCA_001194135.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Octopus sinensis (East Asian common octopus) - GCA_006345805.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Onchocerca volvulus (PRJEB513) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Onthophagus taurus (Dung beetle) - GCA_000648695.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Ooceraea biroi (Clonal raider ant, clonal line C1) - GCA_003672135.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Orbicella faveolata (Mountainous star coral, FL) - GCA_002042975.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Orchesella cincta FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Orussus abietinus (Parasitic wood wasp, OABI.00-Male) - GCA_000612105.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Owenia fusiformis (Segmented worms) - GCA_903813345.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Parasteatoda tepidariorum (Goettingen) - GCA_000365465.3 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Patiria miniata (Bat star starfish, m_02_andy) - GCA_015706575.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Pediculus humanus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Penaeus chinensis (Fleshy prawn) - GCA_019202785.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Penaeus japonicus (Kuruma shrimp, Ginoza2017) - GCA_017312705.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Penaeus monodon (SGIC_2016) - GCA_015228065.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Penaeus vannamei (Pacific white shrimp) - GCA_003789085.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Phlebotomus papatasi FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL GVF VCF VEP Phlebotomus perniciosus (Murcia) - GCA_918844115.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Pocillopora damicornis (RSMAS) - GCA_003704095.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Pogonomyrmex barbatus (Red harvester ant) - GCA_000187915.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Pollicipes pollicipes (Goose neck barnacle, AB1234) - GCA_011947565.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Pomacea canaliculata (SZHN2017) - GCA_003073045.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Pomphorhynchus laevis (P. laevis sensulato, Thorny-headed worm, GPI110) - GCA_012934845.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Portunus trituberculatus (Swimming crab, SZX2019) - GCA_017591435.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Priapulus caudatus (Penis worm) - GCA_000485595.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Pristionchus pacificus (PRJNA12644) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Procambarus clarkii (Red swamp crayfish, Jiangsu) - GCA_020424385.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Rhagoletis pomonella (Grant_MI) - GCA_013731165.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Rhipicephalus microplus (Rmic-2018) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Rhipicephalus sanguineus (Rsan-2018) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Rhodnius prolixus FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Rhopalosiphum maidis (BTI-1) - GCA_003676215.3 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Saccoglossus kowalevskii (Acorn worm) - GCA_000003605.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Sarcoptes scabiei (SSS_KF_BRIS2020) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Schistosoma haematobium (Urinary blood fluke) - GCA_000699445.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Schistosoma mansoni (PRJEA36577) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Sipha flava (LNK) - GCA_003268045.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Solenopsis invicta (M01_SB) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Stegodyphus dumicola (Social spider, AA2019) - GCA_010614865.2 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Stegodyphus mimosarum FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Stomoxys calcitrans FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Strigamia maritima FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Strongylocentrotus purpuratus (Spur 01) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Strongyloides ratti (PRJEB125) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Stylophora pistillata (CSM Monaco) - GCA_002571385.1 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Teleopsis dalmanni (2A) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Tetranychus urticae FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Thelohanellus kitauei FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Tigriopus californicus (San Diego) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Trialeurodes vaporariorum (IVF) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Tribolium castaneum FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Trichinella spiralis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Trichogramma pretiosum (Unisexual culture from Peru) - GCA_000599845.3 FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Trichoplax adhaerens FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Trichuris muris (PRJEB126) FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Varroa destructor FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - VEP Zootermopsis nevadensis FASTA FASTA FASTA FASTA FASTA EMBL GenBank GTF GFF3 TSV RDF JSON MySQL - - 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.
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