Generating eukaryotic reference genome assemblies: Earth BioGenome Project quality standards and recommendations

Kerstin Howe; Dolores R. Agius; Tyler Alioto; Jean-Marc Aury; Roberto Biello; Mark Blaxter; Matthew W. Brown; Tom Brown; Bernat Burriel-Carranza; Haoyu Cheng; Dario Copetti; Solenne Correard; Fernando Cruz; Paul Davis; Aleksandra Denisova; Giulio Formenti; Pedro A. F. Galante; Caroline Howard; Kamil S. Jaron; Erich D. Jarvis; Sergei Kliver; Sergey Koren; Ilia J. Leitch; Harris Lewin; Heng Li; Kerstin Lindblad-Toh; Jack A. Medico; Matthieu Muffato; Zemin Ning; Javan Okendo; Shujun Ou; Marc Palmada-Flores; Brendan J. Pinto; Aurora Ruiz-Herrera; Abdoallah Sharaf; Ying Sims; Jeramiah J. Smith; Marco Sollitto; Cibele G. Sotero-Caio; Marcela Uliano-Silva; Sibelle T. Vilaça; Robert M. Waterhouse; Melissa A. Wilson; Chentao Yang; Guojie Zhang; Chenxi Zhou; Yang Zhou; Richard Durbin

arXiv · 2610.03075

Generating eukaryotic reference genome assemblies: Earth BioGenome Project quality standards and recommendations

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Abstract

Reference genome assemblies are foundational resources across the biological sciences as they begin to expose the fundamental building blocks of each species and the molecular toolkits vital for adaptation and survival. High-quality genomes enable insights into evolution, facilitate ecosystem monitoring and protection and conservation of species, access to new biomaterials and biomedicine, advances in agri- and aquaculture, and support planetary health. The amount of information gathered from a species' genome assembly is directly dependent on its quality. However, different sequencing technologies and software solutions generate a wide range of quality outcomes. Here, the Earth BioGenome Project's Sequencing and Assembly committee, together with a large community of researchers performing eukaryote sequencing and assembly, outlines quality standards for a "reference" assembly and formulates recommendations to ensure these standards are met.

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Kerstin Howe, Dolores R. Agius, Tyler Alioto, Jean-Marc Aury, Roberto Biello, Mark Blaxter, Matthew W. Brown, Tom Brown, Bernat Burriel-Carranza, Haoyu Cheng, Dario Copetti, Solenne Correard, Fernando Cruz, Paul Davis, Aleksandra Denisova, Giulio Formenti, Pedro A. F. Galante, Caroline Howard, Kamil S. Jaron, Erich D. Jarvis, Sergei Kliver, Sergey Koren, Ilia J. Leitch, Harris Lewin, Heng Li, Kerstin Lindblad-Toh, Jack A. Medico, Matthieu Muffato, Zemin Ning, Javan Okendo, Shujun Ou, Marc Palmada-Flores, Brendan J. Pinto, Aurora Ruiz-Herrera, Abdoallah Sharaf, Ying Sims, Jeramiah J. Smith, Marco Sollitto, Cibele G. Sotero-Caio, Marcela Uliano-Silva, Sibelle T. Vilaça, Robert M. Waterhouse, Melissa A. Wilson, Chentao Yang, Guojie Zhang, Chenxi Zhou, Yang Zhou, Richard Durbin. 2026-10-02. Generating eukaryotic reference genome assemblies: Earth BioGenome Project quality standards and recommendations. https://arxiv.org/abs/2610.03075

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