Ensembl Projects

Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. We are based at EMBL-EBI and our software and data are freely available.

The projects listed below incorporate Ensembl code in their displays of genomic data.

Darwin Tree of Life

The Darwin Tree of Life project (DToL) aims to exploit long read technologies to sequence the genomes of all 60,000 species of eukaryotic organisms in Britain and Ireland. It is a collaboration between biodiversity, genomics and analysis partners that hopes to transform the way we do biology, conservation and biotechnology.

Human Pangenome Reference Consortium

The Human Pangenome Reference Consortium aims to sequence 300 individuals, producing a pangenome of 600 haplotypes by around 2024.

European Reference Genome Atlas - Pilot Project

The ERGA Pilot Project is building a pan-European genomics infrastructure that can support the inclusion and equal participation of each European country, at each step of the genome establishment pipeline, from sample collection to publication.

European Reference Genome Atlas (ERGA): Biodiversity Genomics Europe (BGE)

The Biodiversity Genomics Europe (BGE) Project has the overriding aim of accelerating the use of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline.

Vertebrate Genomes Project

The Vertebrate Genomes Project (VGP) aims to generate near error-free reference genome assemblies of ~70,000 extant vertebrate species. These genomes will be used to address fundamental questions in biology and disease, to identify species most genetically at risk for extinction, and to preserve genetic information of life.

Canada BioGenome Project

The Canada BioGenome Project (CBP) aims to make available 400 high quality reference genomes for species in Canada that represent a diverse domain of life.

Aquatic Symbiosis Genomics (ASG) Project

Aquatic Symbiosis Genomics Project is a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts.


AQUA-FAANG is a European project that aims to improve understanding of genome function and exploitation of genotype-to-phenotype prediction in the six most important European farmed fish species.


GENE-SWitCH aims to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken) and to enable immediate translation to the pig and poultry sectors.


The BovReg consortium aims to provide a comprehensive map of functionally active genomic features in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes. This constitutes key knowledge for biology-driven genomic prediction needed by scientific and industry livestock communities.


BLUEPRINT is a large-scale research project that brings together 41 leading European universities, research institutes and industry entrepreneurs in one of the first so-called high impact research initiatives to receive funding from the EU. The goal of BLUEPRINT is to apply highly sophisticated functional genomics analysis to a clearly defined set of primarily human samples from healthy and diseased individuals, and to provide at least 100 reference epigenomes to the scientific community.


NextGen is a collaborative research project investigating the biodiversity of livestock species. NextGen used whole genome sequencing and genotyping microarrays to catalogue and study variation within populations of cattle, sheep and goat.


Quantomics is a large collaborative research project exploring From Sequence to Consequence - Tools for the Exploitation of Livestock Genomes. Quantomics encompasses 17 leading research groups and businesses from 10 countries and is co-financed by the European Commission's 7th Framework Programme.


The HEROIC Project (High-throughput Epigenetic Regulatory Organisation in Chromatin) aims to provide data for research into gene regulation and functioning. This portal site give direct access to sample data, displayed in the Ensembl genome browser.

Neandertal Genome Browser

The Neandertal genome browser displays data from six Neandertal individuals. The 1x coverage reads have been mapped onto the human and chimpanzee reference sequences, rather than being assembled into a full Neandertal genome.