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 "EMBL-EBI Public Data". Data from the Ensembl FTP site can then be found under the "/ensemblorg/pub". You can also click here to open the target directory.

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.ensembl.org 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.

	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)	Regulation (GFF)	Data files	BAM/BigWig
Y	Human Homo sapiens	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV JSON	MySQL	GVF	VCF	VEP	Regulation (GFF)	Regulation data files	BAM/BigWig
Y	Mouse Mus musculus	FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV JSON	MySQL	GVF	VCF	VEP	Regulation (GFF)	Regulation data files	BAM/BigWig
Y		FASTA	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF GFF3	TSV JSON	MySQL	-	-	VEP	-	-	-

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.

JSON

Genome and annotation data in JSON format for each species. 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.