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.

Abstract

© 2018 Nature Publishing Group. All rights reserved. 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). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb). Incorporating an additional 5× coverage of these ultra-long reads 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.

Citation

Jain, M., Koren, S., Miga, K., Quick, J., Rand, A., Sasani, T., Tyson, J., Beggs, A., Dilthey, A., Fiddes, I., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H., Pedersen, B., Rhie, A., Richardson, H., Quinlan, A., Snutch, T., …Loose, M. (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology, 36(4), 338-345. https://doi.org/10.1038/nbt.4060

• Journal Article Type: Article
• Acceptance Date: Dec 11, 2017
• Online Publication Date: Jan 29, 2018
• Publication Date: Apr 1, 2018
• Deposit Date: Feb 5, 2018
• Publicly Available Date: Feb 5, 2018
• Journal: Nature Biotechnology
• Print ISSN: 1087-0156
• Electronic ISSN: 1546-1696
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 36
• Issue: 4
• Pages: 338-345
• DOI: https://doi.org/10.1038/nbt.4060
• Public URL: https://nottingham-repository.worktribe.com/output/907188
• Publisher URL: https://www.nature.com/articles/nbt.4060
• Contract Date: Feb 5, 2018