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

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

in 45/23 / 631/1647/514/1948 / 631/1647/514/2254 / 631/61/212 / Agriculture / Assembly / Bioinformatics / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / DNA sequencing / Gene sequencing / Genome, Human - genetics / Genomes / Genomics / High-Throughput Nucleotide Sequencing - methods / Humans / Life Sciences / Major histocompatibility complex / Methods / Nanopores / Porosity / Sequence Analysis, DNA - methods

2018

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

2018

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2018

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Journal Article

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

Quinlan, Aaron R,

Richardson, Hollian,

Olsen, Hugh E,

Beggs, Andrew D,

Dilthey, Alexander T,

Marriott, Hannah,

Tyson, John R,

Loose, Matthew,

Koren, Sergey,

Loman, Nicholas J,

Rand, Arthur C,

Simpson, Jared T,

Snutch, Terrance P,

Paten, Benedict,

Malla, Sunir,

Pedersen, Brent S,

Jain, Miten,

Quick, Josh,

O'Grady, Justin,

Tee, Louise,

Miga, Karen H,

Rhie, Arang,

Phillippy, Adam M,

Sasani, Thomas A,

Fiddes, Ian T,

Nieto, Tom

2018

Overview

A human genome is sequenced and assembled de novo using a pocket-sized nanopore device. 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.

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Nature Publishing Group US,Nature Publishing Group

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