Towards complete and error-free genome assemblies of all vertebrate species
Authors: Rhie Arang , McCarthy Shane A. , Fedrigo Olivier , Damas Joana , Formenti Giulio , Koren Sergey , Uliano-Silva Marcela , Chow William , Fungtammasan Arkarachai , Gedman Gregory L. , Cantin Lindsey J. , Thibaud-Nissen Francoise , Haggerty Leanne , Lee Chul , Ko Byung June , Kim Juwan , Bista Iliana , Smith Michelle , Haase Bettina , Mountcastle Jacquelyn , Winkler Sylke , Paez Sadye , Howard Jason , Vernes Sonja C. , Lama Tanya M. , Grutzner Frank , Warren Wesley C. , Balakrishnan Christopher , Burt Dave , George Julia M. , Biegler Mathew , Iorns David , Digby Andrew , Eason Daryl , Edwards Taylor , Wilkinson Mark , Turner George , Meyer Axel , Kautt Andreas F. , Franchini Paolo , Detrich H William , Svardal Hannes , Wagner Maximilian , Naylor Gavin J.P. , Pippel Martin , Malinsky Milan , Mooney Mark , Simbirsky Maria , Hannigan Brett T. , Pesout Trevor , Houck Marlys , Misuraca Ann , Kingan Sarah B. , Hall Richard , Kronenberg Zev , Korlach Jonas , Sović Ivan , Dunn Christopher , Ning Zemin , Hastie Alex , Lee Joyce , Selvaraj Siddarth , Green Richard E. , Putnam Nicholas H. , Ghurye Jay , Garrison Erik , Sims Ying , Collins Joanna , Pelan Sarah , Torrance James , Tracey Alan , Wood Jonathan , Guan Dengfeng , London Sarah E. , Clayton David F. , Mello Claudio V. , Friedrich Samantha R. , Lovell Peter V. , Osipova Ekaterina , Al-Ajli Farooq O. , Secomandi Simona , Kim Heebal , Theofanopoulou Constantina , Zhou Yang , Harris Robert S. , Makova Kateryna D. , Medvedev Paul , Hoffman Jinna , Masterson Patrick , Clark Karen , Martin Fergal , Howe Kevin , Flicek Paul , Walenz Brian P. , Kwak Woori , Clawson Hiram , Diekhans Mark , Nassar Luis , Paten Benedict , Kraus Robert H.S. , Lewin Harris , Crawford Andrew J. , Gilbert M. Thomas P. , Zhang Guojie , Venkatesh Byrappa , Murphy Robert W. , Koepfli Klaus-Peter , Shapiro Beth , Johnson Warren E. , Di Palma Federica , Margues-Bonet Tomas , Teeling Emma C. , Warnow Tandy , Graves Jennifer Marshall , Ryder Oliver A. , Hausler David , O’Brien Stephen J. , Howe Kerstin , Myers Eugene W. , Durbin Richard , Phillippy Adam M. , Jarvis Erich D. 
Published: May 2020

AbstractHigh-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 species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6has 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.