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

Human Genome Structural Variation Consortium; 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

doi:10.1038/s41587-020-0719-5

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

Human Genome Structural Variation Consortium, 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 KorbelEvan E Eichler, Tobias Marschall

Research output: Contribution to journal › Article › Academic › peer-review

35 Citations (Scopus)

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Abstract

Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing1,2 with continuous long-read or high-fidelity3 sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.

Original language	English
Pages (from-to)	302-308
Number of pages	13
Journal	Nature Biotechnology
Volume	39
Early online date	7-Dec-2020
DOIs	https://doi.org/10.1038/s41587-020-0719-5
Publication status	Published - Mar-2021
Externally published	Yes

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Fully phased human genome assembly without parental data using single-cell strand sequencing and long readsFinal publisher's version, 4.85 MBLicence: CC BY

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Human Genome Structural Variation Consortium, Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., Marijon, P., Ebler, J., Munson, K. M., Sorensen, M., Sulovari, A., Haukness, M., Ghareghani, M., Lansdorp, P. M., Paten, B., Devine, S. E., Sanders, A. D., Lee, C., Chaisson, M. J. P., ... Marschall, T. (2021). Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nature Biotechnology, 39, 302-308. https://doi.org/10.1038/s41587-020-0719-5

Human Genome Structural Variation Consortium ; Porubsky, David ; Ebert, Peter ; Audano, Peter A ; Vollger, Mitchell R ; Harvey, William T ; Marijon, Pierre ; Ebler, Jana ; Munson, Katherine M ; Sorensen, Melanie ; Sulovari, Arvis ; Haukness, Marina ; Ghareghani, Maryam ; Lansdorp, Peter M ; Paten, Benedict ; Devine, Scott E ; Sanders, Ashley D ; Lee, Charles ; Chaisson, Mark J P ; Korbel, Jan O ; Eichler, Evan E ; Marschall, Tobias. / Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. In: Nature Biotechnology. 2021 ; Vol. 39. pp. 302-308.

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title = "Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads",

abstract = "Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing1,2 with continuous long-read or high-fidelity3 sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.",

author = "{Human Genome Structural Variation Consortium} and David Porubsky and Peter Ebert and Audano, {Peter A} and Vollger, {Mitchell R} and Harvey, {William T} and Pierre Marijon and Jana Ebler and Munson, {Katherine M} and Melanie Sorensen and Arvis Sulovari and Marina Haukness and Maryam Ghareghani and Lansdorp, {Peter M} and Benedict Paten and Devine, {Scott E} and Sanders, {Ashley D} and Charles Lee and Chaisson, {Mark J P} and Korbel, {Jan O} and Eichler, {Evan E} and Tobias Marschall",

year = "2021",

month = mar,

doi = "10.1038/s41587-020-0719-5",

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Human Genome Structural Variation Consortium, Porubsky, D, Ebert, P, Audano, PA, Vollger, MR, Harvey, WT, Marijon, P, Ebler, J, Munson, KM, Sorensen, M, Sulovari, A, Haukness, M, Ghareghani, M, Lansdorp, PM, Paten, B, Devine, SE, Sanders, AD, Lee, C, Chaisson, MJP, Korbel, JO, Eichler, EE & Marschall, T 2021, 'Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads', Nature Biotechnology, vol. 39, pp. 302-308. https://doi.org/10.1038/s41587-020-0719-5

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. / Human Genome Structural Variation Consortium; Porubsky, David; Ebert, Peter; Audano, Peter A; Vollger, Mitchell R; Harvey, William T; Marijon, Pierre; Ebler, Jana; Munson, Katherine M; Sorensen, Melanie; Sulovari, Arvis; Haukness, Marina; Ghareghani, Maryam; Lansdorp, Peter M; Paten, Benedict; Devine, Scott E; Sanders, Ashley D; Lee, Charles; Chaisson, Mark J P; Korbel, Jan O; Eichler, Evan E; Marschall, Tobias.

In: Nature Biotechnology, Vol. 39, 03.2021, p. 302-308.

Research output: Contribution to journal › Article › Academic › peer-review

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AU - Vollger, Mitchell R

AU - Harvey, William T

AU - Marijon, Pierre

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AU - Munson, Katherine M

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AU - Sulovari, Arvis

AU - Haukness, Marina

AU - Ghareghani, Maryam

AU - Lansdorp, Peter M

AU - Paten, Benedict

AU - Devine, Scott E

AU - Sanders, Ashley D

AU - Lee, Charles

AU - Chaisson, Mark J P

AU - Korbel, Jan O

AU - Eichler, Evan E

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JO - Nature Biotechnology

JF - Nature Biotechnology

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