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Nanopore sequencing and assembly of a human genome with ultra-long reads

Jain, M.; Koren, S.; Miga, K.H.; Quick, J.; Rand, A.C.; Sasani, T.A.; Tyson, J.R.; Beggs, A.D.; Dilthey, A.T.; Fiddes, I.T.; Malla, S.; Marriott, H.; Nieto, T.; O'Grady, J.; Olsen, H.E.; Pedersen, B.S.; Rhie, A.; Richardson, H.; Quinlan, A.R.; Snutch, T.P.; Tee, L.; Paten, B.; Phillippy, A.M.; Simpson, J.T.; Loman, N.J.; Loose, M.

Authors

M. Jain

S. Koren

K.H. Miga

J. Quick

A.C. Rand

T.A. Sasani

J.R. Tyson

A.D. Beggs

A.T. Dilthey

I.T. Fiddes

S. Malla

H. Marriott

T. Nieto

J. O'Grady

H.E. Olsen

B.S. Pedersen

A. Rhie

H. Richardson

A.R. Quinlan

T.P. Snutch

L. Tee

B. Paten

A.M. Phillippy

J.T. Simpson

N.J. Loman

M. Loose



Abstract

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38.

Journal Article Type Article
Publication Date Jan 29, 2018
Journal Nature Biotechnology
Print ISSN 1087-0156
Electronic ISSN 1546-1696
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
APA6 Citation Jain, M., Koren, S., Miga, K., Quick, J., Rand, A., Sasani, T., …Loose, M. (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology, https://doi.org/10.1038/nbt.4060
DOI https://doi.org/10.1038/nbt.4060
Publisher URL https://www.nature.com/articles/nbt.4060
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0


nbt.4060.pdf (1.3 Mb)
PDF

Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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