Demo: Exporting whole-genome files from the FTP server

Learn how to download whole-genome sequence and annotation files from Ensembl's FTP folder. This demo was last updated in March 2026.

Ensembl Browser
20 steps
2 minutes

Ensembl

Ebi

Navigate to the [Species Selector](https://beta.ensembl.org/species-selector).

From the lozenges on top, select the species you want to download whole-genome files for. Click [[Human]].

In the assembly information page, click [[Download]] in the Action bar on the right.

The [[Right-hand]] panel lists all whole-genome files available for download. These include: - Full DNA sequence in FASTA - cDNA and peptide sequence in FASTA - Annotation files in GTF, GFF, EMBL and TSV - Variants in VCF - Homologies in TSV

Exporting whole-genome sequences

Click [[FASTA]].

This opens a new tab in your browser and takes you to the file directory in [Ensembl's FTP server](https://ftp.ebi.ac.uk/pub/ensemblorganisms/). FTP You can find your directory path at the top. From this, we can see that we are inside a directory named [[genome]], which is inside a directory named [[GCA_000001405.29]], which is inside a directory named [[Homo_sapiens]], etc.

You can navigate up a directory level by clicking [[Parent Directory]].

This takes you to the parent directory [[GCA_000001405.29]] . Click [[genome/]] to go back to the previous directory.

Each directory lists various files for download. In the [[genome]] directory, you will find the following files: - A folder containing assembly mappings (chain files) - Chromosome lengths in bp as a TSV table - Masked and unmasked DNA sequence in FASTA: - hardmasked (repeat sequences and low-complexity regions are masked and replaced by *N*s) - softmasked (repeat sequences and low-complexity regions are masked and put in lower-case). - unmasked (no repeat and low-complexity regions masked) - md5sum checksums file (used to verify data integrity to confirm files did not get corrupted during download)

Click [[hardmasked.fa.gz]] to download the file.

In the system window, click [[Save]].

Note that file names ending in [[.gz]] are compressed and must be uncompressed/extracted first before opening.

Uncompressed, your FASTA will look something like the screenshot below. Note that repeat sequences and low-complexity regions are masked and replaced by *N*s in in hardmasked FASTA files.

Exporting whole-genome annotation files

Go back to the assembly information page in Ensembl's Species Selector. Let's explore the annotation files. In the right-hand panel, click [[FASTA/GTF/GFF3]].

This opens a new browser tab which takes you to the FTP directory containing annotation files. The following files are available for download: - Annotation files with and without alternative sequences (patches) in EMBL, GFF3 and GTF - Cross references (Xrefs) in TSV - cDNA and peptide sequences in FASTA

Click [[genes.gff3.gz]] to download the whole-genome annotation file in GFF3.

In the system window, click [[Save]].

Uncompressed, your file should look something like the screenshot below. You can read more about GFF3 and its fields in [this Ensembl guide](https://www.ensembl.org/info/website/upload/gff3.html).

You can uncompress [[.gz]] files with the UNIX command `gunzip fileName.gz` .

Exporting whole-genome variation files

Go back to the assembly information page in Ensembl's Species Selector. Let's download the whole-genome variation file. In the right-hand panel, click [[VCF]].

This opens a new browser tab taking you to the FTP directory containing variation files. You can read more about VCF files and the different fields in [this guide](https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#vcf). Click [[variation.vcf.gz]] to download the file.

In your system window, click [[Save]].

Note that whole-genome variation file sizes can be very large. The variation file for human is 210 GB in size.

Demo: Exporting whole-genome files from the FTP server

Learn how to download whole-genome sequence and annotation files from Ensembl's FTP folder. This demo was last updated in March 2026.

Ensembl Browser
20 steps
2 minutes

Ensembl

Ebi

Navigate to the [Species Selector](https://beta.ensembl.org/species-selector).

From the lozenges on top, select the species you want to download whole-genome files for. Click [[Human]].

In the assembly information page, click [[Download]] in the Action bar on the right.

Exporting whole-genome sequences

Click [[FASTA]].

You can navigate up a directory level by clicking [[Parent Directory]].

This takes you to the parent directory [[GCA_000001405.29]] . Click [[genome/]] to go back to the previous directory.

Click [[hardmasked.fa.gz]] to download the file.

In the system window, click [[Save]].

Note that file names ending in [[.gz]] are compressed and must be uncompressed/extracted first before opening.

Uncompressed, your FASTA will look something like the screenshot below. Note that repeat sequences and low-complexity regions are masked and replaced by *N*s in in hardmasked FASTA files.

Exporting whole-genome annotation files

Go back to the assembly information page in Ensembl's Species Selector. Let's explore the annotation files. In the right-hand panel, click [[FASTA/GTF/GFF3]].

Click [[genes.gff3.gz]] to download the whole-genome annotation file in GFF3.

In the system window, click [[Save]].

Uncompressed, your file should look something like the screenshot below. You can read more about GFF3 and its fields in [this Ensembl guide](https://www.ensembl.org/info/website/upload/gff3.html).

You can uncompress [[.gz]] files with the UNIX command `gunzip fileName.gz` .

Exporting whole-genome variation files

Go back to the assembly information page in Ensembl's Species Selector. Let's download the whole-genome variation file. In the right-hand panel, click [[VCF]].

In your system window, click [[Save]].

Note that whole-genome variation file sizes can be very large. The variation file for human is 210 GB in size.