Semi-automated assembly of high-quality diploid human reference genomes
Authors: Jarvis Erich D. , Formenti Giulio , Rhie Arang , Guarracino Andrea , Yang Chentao , Wood Jonathan , Tracey Alan , Thibaud-Nissen Francoise , Vollger Mitchell R. , Porubsky David , Cheng Haoyu , Asri Mobin , Logsdon Glennis A. , Carnevali Paolo , Chaisson Mark J. P. , Chin Chen-Shan , Cody Sarah , Collins Joanna , Ebert Peter , Escalona Merly , Fedrigo Olivier , Fulton Robert S. , Fulton Lucinda L. , Garg Shilpa , Gerton Jennifer L. , Ghurye Jay , Granat Anastasiya , Green Richard E. , Harvey William , Hasenfeld Patrick , Hastie Alex , Haukness Marina , Jaeger Erich B. , Jain Miten , Kirsche Melanie , Kolmogorov Mikhail , Korbel Jan O. , Koren Sergey , Korlach Jonas , Lee Joyce , Li Daofeng , Lindsay Tina , Lucas Julian , Luo Feng , Marschall Tobias , Mitchell Matthew W. , McDaniel Jennifer , Nie Fan , Olsen Hugh E. , Olson Nathan D. , Pesout Trevor , Potapova Tamara , Puiu Daniela , Regier Allison , Ruan Jue , Salzberg Steven L. , Sanders Ashley D. , Schatz Michael C. , Schmitt Anthony , Schneider Valerie A. , Selvaraj Siddarth , Shafin Kishwar , Shumate Alaina , Stitziel Nathan O. , Stober Catherine , Torrance James , Wagner Justin , Wang Jianxin , Wenger Aaron , Xiao Chuanle , Zimin Aleksey V. , Zhang Guojie , Wang Ting , Li Heng , Garrison Erik , Haussler David , Hall Ira , Zook Justin M. , Eichler Evan E. , Phillippy Adam M. , Paten Benedict , Howe Kerstin , Miga Karen H. ,   Human Pangenome Reference Consortium
Published: October 2022

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent–child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.