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

By Miten Jain, S Koren, Josh Quick, AC Rand, TA Sasani, JR Tyson, Andrew D Beggs, AT Dilthey, IT Fiddes, S Malla, H Marriott, KH Miga, T Nieto, J O’Grady, HE Olsen, BS Pedersen, A Rhie, H Richardson, AR Quinlan, TP Snutch, L. Tee, B Paten, AM Phillippy, JT Simpson, NJ Loman, Matthew W Loose

Posted 20 Apr 2017
bioRxiv DOI: 10.1101/128835 (published DOI: 10.1038/nbt.4060)

Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. However until recently nanopore sequencing has been mainly applied to small genomes, due to the limited output attainable. We present nanopore sequencing and assembly of the GM12878 Utah/Ceph human reference genome generated using the Oxford Nanopore MinION and R9.4 version chemistry. We generated 91.2 Gb of sequence data (~30x theoretical coverage) from 39 flowcells. De novo assembly yielded a highly complete and contiguous assembly (NG50 ~3Mb). We observed considerable variability in homopolymeric tract resolution between different basecallers. The data permitted sensitive detection of both large structural variants and epigenetic modifications. Further we developed a new approach exploiting the long-read capability of this system and found that adding an additional 5x-coverage of "ultra-long" reads (read N50 of 99.7kb) more than doubled the assembly contiguity. Modelling the repeat structure of the human genome predicts extraordinarily contiguous assemblies may be possible using nanopore reads alone. Portable de novo sequencing of human genomes may be important for rapid point-of-care diagnosis of rare genetic diseases and cancer, and monitoring of cancer progression. The complete dataset including raw signal is available as an Amazon Web Services Open Dataset at: https://github.com/nanopore-wgs-consortium/NA12878.

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