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

Multi-species data

DatabaseMySQLTSVEMFMAFXML
Pan_compara Multi-speciesMySQLTSVEMFXML
Plants 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)
YArabidopsis thalianaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YOryza sativa Japonica GroupFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YTriticum aestivumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YHordeum vulgareFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YZea maysFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YPhyscomitrium patensFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Actinidia chinensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aegilops tauschiiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Amborella trichopodaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ananas comosusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Arabidopsis halleriFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Arabidopsis lyrataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Arabis alpinaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Asparagus officinalisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Beta vulgarisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Brachypodium distachyonFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Brassica napusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Brassica oleraceaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Brassica rapaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Camelina sativaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cannabis sativa femaleFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Capsicum annuumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Chara brauniiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Chenopodium quinoaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Chlamydomonas reinhardtiiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Chondrus crispusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Citrullus lanatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Citrus clementinaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Coffea canephoraFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Corchorus capsularisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cucumis meloFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cucumis sativusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cyanidioschyzon merolaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cynara cardunculusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Daucus carotaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dioscorea rotundataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eragrostis curvulaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eragrostis tefFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eucalyptus grandisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eutrema salsugineumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Galdieria sulphurariaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glycine maxFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Gossypium raimondiiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Helianthus annuusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Hordeum vulgare GoldenPromiseFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hordeum vulgare TRITEXFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ipomoea trilobaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Juglans regiaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Kalanchoe fedtschenkoiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leersia perrieriFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lupinus angustifoliusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Malus domestica GoldenFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Manihot esculentaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Marchantia polymorphaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Medicago truncatulaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Musa acuminataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nicotiana attenuataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nymphaea colorataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Olea europaea var. sylvestrisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza barthiiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza brachyanthaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza glaberrimaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Oryza glumipatulaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Oryza longistaminataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza meridionalisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza nivaraFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza punctataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza rufipogonFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oryza sativa Indica GroupFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Ostreococcus lucimarinusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Panicum hallii FIL2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Panicum hallii HAL2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Papaver somniferumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phaseolus vulgarisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pistacia veraFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Populus trichocarpaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Prunus aviumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Prunus dulcisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Prunus persicaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Quercus lobataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Rosa chinensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Saccharum spontaneumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Selaginella moellendorffiiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Sesamum indicumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Setaria italicaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Setaria viridisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Solanum lycopersicumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Solanum tuberosumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Solanum tuberosum RH89-039-16FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Sorghum bicolorFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Theobroma cacao Belizian Criollo B97-61/B2FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Theobroma cacao Matina 1-6FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trifolium pratenseFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum ArinalrforFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum CadenzaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum ClaireFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum JaggerFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum JuliusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum LancerFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum LandmarkFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum MaceFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum Norin61FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum ParagonFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum RobigusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum StanleyFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum Sy MattisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum aestivum WeebillFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum dicoccoidesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum speltaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Triticum turgidumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Triticum urartuFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Vigna angularisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Vigna radiataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Vitis viniferaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP

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. /current/plants/.

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.