Literature DB >> 35332338

Haplotype-resolved assembly of diploid genomes without parental data.

Haoyu Cheng1,2, Erich D Jarvis3,4, Olivier Fedrigo3, Klaus-Peter Koepfli5,6,7, Lara Urban8, Neil J Gemmell8, Heng Li9,10.   

Abstract

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.
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

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Year:  2022        PMID： 35332338      PMCID： PMC9464699          DOI： 10.1038/s41587-022-01261-x

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   68.164


  19 in total

1.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Authors:  Felipe A Simão; Robert M Waterhouse; Panagiotis Ioannidis; Evgenia V Kriventseva; Evgeny M Zdobnov
Journal:  Bioinformatics       Date:  2015-06-09       Impact factor: 6.937

2.  Phased diploid genome assembly with single-molecule real-time sequencing.

Authors:  Chen-Shan Chin; Paul Peluso; Fritz J Sedlazeck; Maria Nattestad; Gregory T Concepcion; Alicia Clum; Christopher Dunn; Ronan O'Malley; Rosa Figueroa-Balderas; Abraham Morales-Cruz; Grant R Cramer; Massimo Delledonne; Chongyuan Luo; Joseph R Ecker; Dario Cantu; David R Rank; Michael C Schatz
Journal:  Nat Methods       Date:  2016-10-17       Impact factor: 28.547

3.  HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Authors:  Sergey Nurk; Brian P Walenz; Arang Rhie; Mitchell R Vollger; Glennis A Logsdon; Robert Grothe; Karen H Miga; Evan E Eichler; Adam M Phillippy; Sergey Koren
Journal:  Genome Res       Date:  2020-08-14       Impact factor: 9.043

Review 4.  Long-read human genome sequencing and its applications.

Authors:  Glennis A Logsdon; Mitchell R Vollger; Evan E Eichler
Journal:  Nat Rev Genet       Date:  2020-06-05       Impact factor: 53.242

5.  Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.

Authors:  David Porubsky; Peter Ebert; Peter A Audano; Mitchell R Vollger; William T Harvey; Pierre Marijon; Jana Ebler; Katherine M Munson; Melanie Sorensen; Arvis Sulovari; Marina Haukness; Maryam Ghareghani; Peter M Lansdorp; Benedict Paten; Scott E Devine; Ashley D Sanders; Charles Lee; Mark J P Chaisson; Jan O Korbel; Evan E Eichler; Tobias Marschall
Journal:  Nat Biotechnol       Date:  2020-12-07       Impact factor: 54.908

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

Authors:  Arang Rhie; Shane A McCarthy; Olivier Fedrigo; Joana Damas; Giulio Formenti; Sergey Koren; Marcela Uliano-Silva; William Chow; Arkarachai Fungtammasan; Juwan Kim; Chul Lee; Byung June Ko; Mark Chaisson; Gregory L Gedman; Lindsey J Cantin; Francoise Thibaud-Nissen; Leanne Haggerty; 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; Dave Burt; Julia M George; Matthew T Biegler; David Iorns; Andrew Digby; Daryl Eason; Bruce Robertson; Taylor Edwards; Mark Wilkinson; George 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 Kronenberg; Ivan Sović; Christopher Dunn; Zemin Ning; Alex Hastie; Joyce Lee; Siddarth Selvaraj; Richard E Green; Nicholas H Putnam; Ivo Gut; Jay Ghurye; Erik Garrison; Ying Sims; Joanna Collins; Sarah Pelan; James Torrance; Alan Tracey; Jonathan Wood; Robel E Dagnew; 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; Michael Hiller; Yang Zhou; Robert S Harris; Kateryna D 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; 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 Marques-Bonet; Emma C Teeling; Tandy Warnow; Jennifer Marshall Graves; Oliver A Ryder; David Haussler; Stephen J O'Brien; Jonas Korlach; Harris A Lewin; Kerstin Howe; Eugene W Myers; Richard Durbin; Adam M Phillippy; Erich D Jarvis
Journal:  Nature       Date:  2021-04-28       Impact factor: 49.962

7.  Curated variation benchmarks for challenging medically relevant autosomal genes.

Authors:  Chen-Shan Chin; Justin M Zook; Fritz J Sedlazeck; Justin Wagner; Nathan D Olson; Lindsay Harris; Jennifer McDaniel; Haoyu Cheng; Arkarachai Fungtammasan; Yih-Chii Hwang; Richa Gupta; Aaron M Wenger; William J Rowell; Ziad M Khan; Jesse Farek; Yiming Zhu; Aishwarya Pisupati; Medhat Mahmoud; Chunlin Xiao; Byunggil Yoo; Sayed Mohammad Ebrahim Sahraeian; Danny E Miller; David Jáspez; José M Lorenzo-Salazar; Adrián Muñoz-Barrera; Luis A Rubio-Rodríguez; Carlos Flores; Giuseppe Narzisi; Uday Shanker Evani; Wayne E Clarke; Joyce Lee; Christopher E Mason; Stephen E Lincoln; Karen H Miga; Mark T W Ebbert; Alaina Shumate; Heng Li
Journal:  Nat Biotechnol       Date:  2022-02-07       Impact factor: 68.164

8.  Identifying and removing haplotypic duplication in primary genome assemblies.

Authors:  Dengfeng Guan; Shane A McCarthy; Jonathan Wood; Kerstin Howe; Yadong Wang; Richard Durbin
Journal:  Bioinformatics       Date:  2020-05-01       Impact factor: 6.937

9.  The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.

Authors:  Kang Du; Matthias Stöck; Susanne Kneitz; Christophe Klopp; Joost M Woltering; Mateus Contar Adolfi; Romain Feron; Dmitry Prokopov; Alexey Makunin; Ilya Kichigin; Cornelia Schmidt; Petra Fischer; Heiner Kuhl; Sven Wuertz; Jörn Gessner; Werner Kloas; Cédric Cabau; Carole Iampietro; Hugues Parrinello; Chad Tomlinson; Laurent Journot; John H Postlethwait; Ingo Braasch; Vladimir Trifonov; Wesley C Warren; Axel Meyer; Yann Guiguen; Manfred Schartl
Journal:  Nat Ecol Evol       Date:  2020-03-30       Impact factor: 15.460

10.  De novo assembly of haplotype-resolved genomes with trio binning.

Authors:  Sergey Koren; Arang Rhie; Brian P Walenz; Alexander T Dilthey; Derek M Bickhart; Sarah B Kingan; Stefan Hiendleder; John L Williams; Timothy P L Smith; Adam M Phillippy
Journal:  Nat Biotechnol       Date:  2018-10-22       Impact factor: 54.908
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  5 in total

1.  Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies.

Authors:  Alexander S Leonard; Danang Crysnanto; Zih-Hua Fang; Michael P Heaton; Brian L Vander Ley; Carolina Herrera; Heinrich Bollwein; Derek M Bickhart; Kristen L Kuhn; Timothy P L Smith; Benjamin D Rosen; Hubert Pausch
Journal:  Nat Commun       Date:  2022-05-31       Impact factor: 17.694

Review 2.  Recent Advances in Renal Medullary Carcinoma.

Authors:  Yongdong Su; Andrew L Hong
Journal:  Int J Mol Sci       Date:  2022-06-26       Impact factor: 6.208

3.  Widespread false gene gains caused by duplication errors in genome assemblies.

Authors:  Byung June Ko; Chul Lee; Juwan Kim; Arang Rhie; Dong Ahn Yoo; Kerstin Howe; Jonathan Wood; Seoae Cho; Samara Brown; Giulio Formenti; Erich D Jarvis; Heebal Kim
Journal:  Genome Biol       Date:  2022-09-27       Impact factor: 17.906

4.  Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs.

Authors:  Giulio Formenti; Linelle Abueg; Angelo Brajuka; Nadolina Brajuka; Cristóbal Gallardo-Alba; Alice Giani; Olivier Fedrigo; Erich D Jarvis
Journal:  Bioinformatics       Date:  2022-07-07       Impact factor: 6.931

5.  False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.

Authors:  Juwan Kim; Chul Lee; Byung June Ko; Dong Ahn Yoo; Sohyoung Won; Adam M Phillippy; Olivier Fedrigo; Guojie Zhang; Kerstin Howe; Jonathan Wood; Richard Durbin; Giulio Formenti; Samara Brown; Lindsey Cantin; Claudio V Mello; Seoae Cho; Arang Rhie; Heebal Kim; Erich D Jarvis
Journal:  Genome Biol       Date:  2022-09-27       Impact factor: 17.906
  5 in total

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