Ensembl 2021

Abstract

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

Figure 1.

Growth and representation of genomes in Ensembl. Top panel: Ensembl genome counts for the 10 most recent Ensembl releases. Since Ensembl release 92 (April 2018), we have nearly tripled the number of genomes we support. Lower panel: distribution of current chordate genomes in Ensembl, by clade.

Figure 2.

The Blueprint Signal Track Hub. The primary dimensions of the Hub, Sample description and Experiment, are used to create the track selection matrix. Other dimensions within the data are shown in a panel on the right (e.g. Analysis group and Analysis Type), and tracks can be filtered by clicking on any of the types within those. Even greater granularity of track selection can be achieved by selecting tracks from a pop-up menu associated with each individual cell of the matrix.