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Yates AD, Allen J, Amode RM, et al. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Res. 2022;50:D996-D1003doi: 10.1093/nar/gkab1007.
Yates, A. D., Allen, J., Amode, R. M., Azov, A. G., Barba, M., Becerra, A., Bhai, J., Campbell, L. I., Carbajo Martinez, M., Chakiachvili, M., Chougule, K., Christensen, M., Contreras-Moreira, B., Cuzick, A., Da Rin Fioretto, L., Davis, P., De Silva, N. H., Diamantakis, S., Dyer, S., Elser, J., Filippi, C. V., Gall, A., Grigoriadis, D., Guijarro-Clarke, C., Gupta, P., Hammond-Kosack, K. E., Howe, K. L., Jaiswal, P., Kaikala, V., Kumar, V., Kumari, S., Langridge, N., Le, T., Luypaert, M., Maslen, G. L., Maurel, T., Moore, B., Muffato, M., Mushtaq, A., Naamati, G., Naithani, S., Olson, A., Parker, A., Paulini, M., Pedro, H., Perry, E., Preece, J., Quinton-Tulloch, M., Rodgers, F., Rosello, M., Ruffier, M., Seager, J., Sitnik, V., Szpak, M., Tate, J., Tello-Ruiz, M. K., Trevanion, S. J., Urban, M., Ware, D., Wei, S., Williams, G., Winterbottom, A., Zarowiecki, M., Finn, R. D., & Flicek, P. (2022). Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic acids research, 50D996-D1003. https://doi.org/10.1093/nar/gkab1007
Yates, Andrew D, et al. "Ensembl Genomes 2022: an expanding genome resource for non-vertebrates." Nucleic acids research vol. 50 (2022): D996-D1003. doi: https://doi.org/10.1093/nar/gkab1007
Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, Davis P, De Silva NH, Diamantakis S, Dyer S, Elser J, Filippi CV, Gall A, Grigoriadis D, Guijarro-Clarke C, Gupta P, Hammond-Kosack KE, Howe KL, Jaiswal P, Kaikala V, Kumar V, Kumari S, Langridge N, Le T, Luypaert M, Maslen GL, Maurel T, Moore B, Muffato M, Mushtaq A, Naamati G, Naithani S, Olson A, Parker A, Paulini M, Pedro H, Perry E, Preece J, Quinton-Tulloch M, Rodgers F, Rosello M, Ruffier M, Seager J, Sitnik V, Szpak M, Tate J, Tello-Ruiz MK, Trevanion SJ, Urban M, Ware D, Wei S, Williams G, Winterbottom A, Zarowiecki M, Finn RD, Flicek P. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Res. 2022 Jan 07;50:D996-D1003. doi: 10.1093/nar/gkab1007. PMID: 34791415; PMCID: PMC8728113.
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Nucleic Acids Res. 2022 Jan 07;50:D996-D1003. doi: 10.1093/nar/gkab1007.

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Nucleic acids research

Andrew D Yates, James Allen, Ridwan M Amode, Andrey G Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel Christensen, Bruno Contreras-Moreira, Alayne Cuzick, Luca Da Rin Fioretto, Paul Davis, Nishadi H De Silva, Stavros Diamantakis, Sarah Dyer, Justin Elser, Carla V Filippi, Astrid Gall, Dionysios Grigoriadis, Cristina Guijarro-Clarke, Parul Gupta, Kim E Hammond-Kosack, Kevin L Howe, Pankaj Jaiswal, Vinay Kaikala, Vivek Kumar, Sunita Kumari, Nick Langridge, Tuan Le, Manuel Luypaert, Gareth L Maslen, Thomas Maurel, Benjamin Moore, Matthieu Muffato, Aleena Mushtaq, Guy Naamati, Sushma Naithani, Andrew Olson, Anne Parker, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Mark Quinton-Tulloch, Faye Rodgers, Marc Rosello, Magali Ruffier, James Seager, Vasily Sitnik, Michal Szpak, John Tate, Marcela K Tello-Ruiz, Stephen J Trevanion, Martin Urban, Doreen Ware, Sharon Wei, Gary Williams, Andrea Winterbottom, Magdalena Zarowiecki, Robert D Finn, Paul Flicek

Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  2. Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
  3. Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK.
  4. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
  5. Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina.
  6. Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina.
  7. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
  8. USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA.

PMID: 34791415 PMCID: PMC8728113 DOI: 10.1093/nar/gkab1007

Abstract

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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