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

Miten Jain, Sergey Koren, Karen H. Miga, Josh Quick, Arthur C. Rand, Thomas A. Sasani, John R. Tyson, Andrew D. Beggs, Alexander T. Dilthey, Ian T. Fiddes, Sunir Malla, Hannah Marriott, Tom Nieto, Justin O'Grady, Hugh E. Olson, Brent S. Pedersen, Arang Rhie, Hollian Richardson, Aaron R. Quinlan, Terrance P. SnutchLouise Tee, Benedict Paten, Adam M. Phillippy, Jared T. Simpson, Nicholas J. Loman, Matthew Loose

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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.
Original languageEnglish
Pages (from-to)338–345
Number of pages8
JournalNature Biotechnology
Early online date29 Jan 2018
Publication statusPublished - Jan 2018

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