Haplotype-resolved assembly of diploid genomes without parental data

被引：285

作者：

Cheng, Haoyu ^{[1
,2
]}

Jarvis, Erich D. ^{[3
,4
]}

Fedrigo, Olivier ^{[3
]}

Koepfli, Klaus-Peter ^{[5
,6
,7
]}

Urban, Lara ^{[8
]}

Gemmell, Neil J. ^{[8
]}

Li, Heng ^{[1
,2
]}

机构：

[1] Dana Farber Canc Inst, Dept Data Sci, Boston, MA 02115 USA

[2] Harvard Med Sch, Dept Biomed Informat, Boston, MA 02115 USA

[3] Rockefeller Univ, Vertebrate Genome Lab, 1230 York Ave, New York, NY 10021 USA

[4] Howard Hughes Med Inst, Chevy Chase, MD USA

[5] George Mason Univ, Smithsonian Mason Sch Conservat, Front Royal, VA USA

[6] Smithsonian Conservat Biol Inst, Ctr Species Survival, Natl Zool Pk, Washington, DC USA

[7] ITMO Univ, Comp Technol Lab, St Petersburg, Russia

[8] Univ Otago, Dept Anat, Dunedin, New Zealand

来源：

NATURE BIOTECHNOLOGY | 2022年 / 40卷 / 09期

基金：

美国国家卫生研究院;

关键词：

20;

D O I：

10.1038/s41587-022-01261-x

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Routine haplotype-resolved genome assembly from single samples remains an unresolved problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of similar quality to the best pedigree-based assemblies.

引用

页码：1332 / +

页数：7

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