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Towards complete and error-free genome assemblies of all vertebrate species

By Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Chul Lee, Byung June Ko, Juwan Kim, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, D.W. Burt, Julia M. George, Mathew Biegler, David Iorns, Andrew Digby, Daryl Eason, Taylor Edwards, Mark Wilkinson, George F. Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J.P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev N. Kronenberg, Jonas Korlach, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Yang Zhou, Robert S. Harris, Kateryna Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H.S. Kraus, Harris A. Lewin, Andrew J. Crawford, M. Thomas P Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Margues-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer A Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O’Brien, Kerstin Howe, Eugene W Myers, Richard Durbin, Adam M. Phillippy, Erich D. Jarvis

Posted 23 May 2020
bioRxiv DOI: 10.1101/2020.05.22.110833

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species. To address this issue, the international Genome 10K (G10K) consortium has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences. ### Competing Interest Statement During the contributing period, B.T.H, M.Si., A.F. and M.Mo. were employees of DNAnexus Inc. S.B.K., R.H., Z.K., J.Ko., I.S. and C.D. are full-time employees at Pacific Biosciences, a company developing single-molecule sequencing technologies. R.D. is a scientific advisory board member of Dovetail Inc. P.Fl. is a member of the Scientific Advisory Boards of Fabric Genomics, Inc., and Eagle Genomics, Ltd. H.C. receives royalties from the sale of UCSC Genome Browser source code, LiftOver, GBiB, and GBiC licenses to commercial entities. S.K has received travel funds to speak at symposia organized by Oxford Nanopore. M.D. and L.N. receives royalties from licensing of UCSC Genome Browser. For W.E.J., the content here is not to be construed as the views of the DA or DOD.

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