Ensembl Rapid Release

Ensembl logo on blue background

Ensembl Rapid Release

29 Jun 2020 - 13:12

The Ensembl team is excited to announce the launch of the Ensembl Rapid Release website. Ensembl Rapid Release is a new, lightweight genome browser designed to allow quick release of the latest genome annotation for a large number of vertebrate and non-vertebrate species.

Advancements in new sequencing technologies means that genome sequencing and assembly are faster and cheaper than ever before. With the huge increase in sequencing planned by large biodiversity initiatives such as Darwin Tree of Life, the Vertebrate Genomes Project and the Earth BioGenome Project, alongside the work of smaller groups and communities, high quality genome assemblies for hundreds (and soon thousands) of different species are being produced and made publicly available at an ever-increasing rate.

The new Ensembl Rapid Release genome browser and databases aim to provide annotation for these recently produced, publicly available vertebrate and non-vertebrate genomes as quickly as possible.

Figue 1. The Ensembl Rapid Release homepage

Importantly, Ensembl Rapid Release runs a short data release cycle, where new genome sequences and annotation are added every two weeks. This differs from the release cycle on the Ensembl genome browser, where releases occur approximately every three months.

There are also important differences between the available data and overall functionality in Ensembl Rapid Release compared to the main Ensembl genome browser. A traditional Ensembl release combines the gene set with comparative data (gene trees, gene names and genome alignments) and, where available, variation and regulation data. On the other hand, Ensembl Rapid Release currently only focuses on the gene set and functionality, such as programmatic access and data archiving, are not present. These are important limitations to consider when using Ensembl Rapid Release.

The data and functionality currently provided by Ensembl Rapid Release include:

  • Gene annotation with Ensembl stable IDs
  • Repeat annotation
  • Protein feature annotation
  • BLAST functionality
  • File dumps including transcript and protein sequences and the softmasked genome sequence through the Ensembl Rapid Release FTP site.
Figure 2. The Ensembl Rapid Release data views includes (A) the Location view, (B) the Gene tab and (C) the Transcript tab. 

In addition to direct access to all genome-wide flat files through the FTP site, users can browse available files and find quick links to download gene annotation and genome sequence files through the species table, where there is also assembly and annotation statistics.

Figure 3. The Ensembl Rapid Release species table, showing assembly and annotation statistics and links to download gene annotation and genome sequence files via the FTP site.
  Over the coming months the Ensembl team intends to increase the range of data types and functionality presented in Ensembl Rapid Release; including basic homology data, gene names and programmatic access. If you have any feedback or questions about the Ensembl Rapid Release genome browser and databases, please do not hesitate to get in touch via the Ensembl Helpdesk. This post was originally published on the Ensembl blog.

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