H
Haoyu Cheng
Researcher at Harvard University
Publications - 18
Citations - 1491
Haoyu Cheng is an academic researcher from Harvard University. The author has contributed to research in topics: Sequence assembly & Medicine. The author has an hindex of 6, co-authored 11 publications receiving 344 citations. Previous affiliations of Haoyu Cheng include Dana Corporation.
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
TL;DR: Hifiasm as discussed by the authors is a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph.
Journal ArticleDOI
Haplotype-resolved de novo assembly with phased assembly graphs
TL;DR: Hifiasm is described, a new de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph and strives to preserve the contiguity of all haplotypes.
Journal ArticleDOI
Chromosome-scale, haplotype-resolved assembly of human genomes.
Shilpa Garg,Arkarachai Fungtammasan,Andrew Carroll,Mike Chou,Anthony D. Schmitt,Xiang Zhou,Stephen Mac,Paul Peluso,Emily Hatas,Jay Ghurye,Jared Maguire,Medhat Mahmoud,Haoyu Cheng,David Heller,Justin M. Zook,Tobias Moemke,Tobias Marschall,Tobias Marschall,Fritz J. Sedlazeck,John Aach,Chen-Shan Chin,George M. Church,Heng Li +22 more
TL;DR: A method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day, outperforming other approaches in terms of both contiguity and phasing completeness.
Journal ArticleDOI
Haplotype-resolved assembly of diploid genomes without parental data
Haoyu Cheng,Erich D. Jarvis,Olivier Fedrigo,Klaus-Peter Koepfli,Lara Urban,Neil J. Gemmell,Heng Li +6 more
TL;DR: In this article , the authors 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.
Journal ArticleDOI
A draft human pangenome reference
Wen-Wei Liao,Mobin Asri,Jana Ebler,Daniel Doerr,Marina Haukness,Glenn Hickey,Shuangjia Lu,Julian K. Lucas,Jean Marcel Maurice Monlong,Haley J. Abel,Silvia Buonaiuto,Xian Chang,Haoyu Cheng,Justin Jang Hann Chu,Vincenza Colonna,Jordan M. Eizenga,Xiaowen Feng,Christian Fischer,Robert S. Fulton,Shilpa Garg,Cristian Groza,Andrea Guarracino,William T. Harvey,Simon Heumos,Kerstin Howe,Miten Jain,Tsung-Yu Lu,Charles Markello,Fergal J. Martin,Matthew Mitchell,Katherine M. Munson,Moses N. Mwaniki,Adam M. Novak,Hugh E. Olsen,Trevor Pesout,David Porubsky,Pjotr Prins,Jonas Andreas Sibbesen,Chad Tomlinson,Flavia Villani,Mitchell R. Vollger,Guillaume Bourque,Mark Chaisson,Paul Flicek,Adam M. Phillippy,Justin M. Zook,Evan E. Eichler,David Haussler,Erich D. Jarvis,Karen H. Miga,Ting Wang,Erik Garrison,Tobias Marschall,Ira M. Hall,Heng Li,Benedict Paten +55 more
TL;DR: The pangenome reference as discussed by the authors contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals and is more than 99% accurate at the structural and base pair levels.