Ensembl 2022

Author:

Cunningham Fiona1ORCID,Allen James E1,Allen Jamie1,Alvarez-Jarreta Jorge1,Amode M Ridwan1,Armean Irina M1ORCID,Austine-Orimoloye Olanrewaju1,Azov Andrey G1,Barnes If1,Bennett Ruth1,Berry Andrew1,Bhai Jyothish1,Bignell Alexandra1,Billis Konstantinos1ORCID,Boddu Sanjay1,Brooks Lucy1,Charkhchi Mehrnaz1,Cummins Carla1ORCID,Da Rin Fioretto Luca1,Davidson Claire1,Dodiya Kamalkumar1,Donaldson Sarah1,El Houdaigui Bilal1,El Naboulsi Tamara1,Fatima Reham1,Giron Carlos Garcia1ORCID,Genez Thiago1,Martinez Jose Gonzalez1,Guijarro-Clarke Cristina1,Gymer Arthur1,Hardy Matthew1,Hollis Zoe1,Hourlier Thibaut1ORCID,Hunt Toby1,Juettemann Thomas1ORCID,Kaikala Vinay1,Kay Mike1,Lavidas Ilias1,Le Tuan1,Lemos Diana1,Marugán José Carlos1,Mohanan Shamika1,Mushtaq Aleena1,Naven Marc1,Ogeh Denye N1,Parker Anne1,Parton Andrew1,Perry Malcolm1,Piližota Ivana1,Prosovetskaia Irina1,Sakthivel Manoj Pandian1,Salam Ahamed Imran Abdul1,Schmitt Bianca M1,Schuilenburg Helen1,Sheppard Dan1,Pérez-Silva José G1,Stark William1,Steed Emily1,Sutinen Kyösti1,Sukumaran Ranjit1,Sumathipala Dulika1,Suner Marie-Marthe1ORCID,Szpak Michal1,Thormann Anja1,Tricomi Francesca Floriana1,Urbina-Gómez David1,Veidenberg Andres1,Walsh Thomas A1,Walts Brandon1,Willhoft Natalie1,Winterbottom Andrea1,Wass Elizabeth1,Chakiachvili Marc1,Flint Bethany1,Frankish Adam1ORCID,Giorgetti Stefano1,Haggerty Leanne1,Hunt Sarah E1ORCID,IIsley Garth R1,Loveland Jane E1ORCID,Martin Fergal J1ORCID,Moore Benjamin1,Mudge Jonathan M1,Muffato Matthieu1,Perry Emily1ORCID,Ruffier Magali1ORCID,Tate John1,Thybert David1,Trevanion Stephen J1,Dyer Sarah1,Harrison Peter W1ORCID,Howe Kevin L1ORCID,Yates Andrew D1ORCID,Zerbino Daniel R1ORCID,Flicek Paul1ORCID

Affiliation:

1. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Abstract

Abstract Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Funder

Wellcome Trust

National Human Genome Research Institute

Biotechnology and Biological Sciences Research Council

British Council

European Molecular Biology Laboratory

European Union's Horizon 2020 research and innovation programme

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference35 articles.

1. The Ensembl Variant Effect Predictor;McLaren;Genome Biol.,2016

2. Ensembl 2021;Howe;Nucleic. Acids. Res.,2021

3. Towards complete and error-free genome assemblies of all vertebrate species;Rhie;Nature,2021

4. Earth BioGenome Project: Sequencing life for the future of life;Lewin;Proc. Natl. Acad. Sci. U.S.A.,2018

5. STAR: ultrafast universal RNA-seq aligner;Dobin;Bioinformatics,2013

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