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

Miten Jain, S Koren, J Quick, AC Rand, TA Sasani, JR Tyson, AD 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, View ORCID ProfileM Loose
doi: https://doi.org/10.1101/128835
Miten Jain
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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S Koren
2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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J Quick
3Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
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AC Rand
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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TA Sasani
4Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
5USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
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JR Tyson
7Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
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AD Beggs
8Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, UK
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AT Dilthey
2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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IT Fiddes
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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S Malla
9DeepSeq, School of Life Sciences, University of Nottingham, UK
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H Marriott
9DeepSeq, School of Life Sciences, University of Nottingham, UK
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KH Miga
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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T Nieto
8Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, UK
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J O’Grady
10Norwich Medical School, University of East Anglia, Norwich, UK
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HE Olsen
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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BS Pedersen
4Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
5USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
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A Rhie
2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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H Richardson
10Norwich Medical School, University of East Anglia, Norwich, UK
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AR Quinlan
4Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
5USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
6Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
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TP Snutch
7Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
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L Tee
8Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, UK
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B Paten
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
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AM Phillippy
2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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JT Simpson
11Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada
12Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada
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NJ Loman
3Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
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  • For correspondence: n.j.loman@bham.ac.uk matt.loose@nottingham.ac.uk
M Loose
9DeepSeq, School of Life Sciences, University of Nottingham, UK
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  • ORCID record for M Loose
  • For correspondence: n.j.loman@bham.ac.uk matt.loose@nottingham.ac.uk
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Abstract

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 (∼30× 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 5×-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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 20, 2017.
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain, S Koren, J Quick, AC Rand, TA Sasani, JR Tyson, AD 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, M Loose
bioRxiv 128835; doi: https://doi.org/10.1101/128835
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain, S Koren, J Quick, AC Rand, TA Sasani, JR Tyson, AD 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, M Loose
bioRxiv 128835; doi: https://doi.org/10.1101/128835

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