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

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 la... Full description

Journal Title: Nature biotechnology April 2018, Vol.36(4), pp.338-345
Main Author: Jain, Miten
Other Authors: Koren, Sergey , Miga, Karen H , Quick, Josh , Rand, Arthur C , Sasani, Thomas A , Tyson, John R , Beggs, Andrew D , Dilthey, Alexander T , Fiddes, Ian T , Malla, Sunir , Marriott, Hannah , Nieto, Tom , O'Grady, Justin , Olsen, Hugh E , Pedersen, Brent S , Rhie, Arang , Richardson, Hollian , Quinlan, Aaron R , Snutch, Terrance P , Tee, Louise , Paten, Benedict , Phillippy, Adam M , Simpson, Jared T , Loman, Nicholas J , Loose, Matthew
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1546-1696 ; PMID: 29431738 Version:1 ; DOI: 10.1038/nbt.4060
Link: http://pubmed.gov/29431738
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recordid: medline29431738
title: Nanopore sequencing and assembly of a human genome with ultra-long reads
format: Article
creator:
  • Jain, Miten
  • Koren, Sergey
  • Miga, Karen H
  • Quick, Josh
  • Rand, Arthur C
  • Sasani, Thomas A
  • Tyson, John R
  • Beggs, Andrew D
  • Dilthey, Alexander T
  • Fiddes, Ian T
  • Malla, Sunir
  • Marriott, Hannah
  • Nieto, Tom
  • O'Grady, Justin
  • Olsen, Hugh E
  • Pedersen, Brent S
  • Rhie, Arang
  • Richardson, Hollian
  • Quinlan, Aaron R
  • Snutch, Terrance P
  • Tee, Louise
  • Paten, Benedict
  • Phillippy, Adam M
  • Simpson, Jared T
  • Loman, Nicholas J
  • Loose, Matthew
subjects:
  • Genomics
  • Genome, Human -- Genetics
  • High-Throughput Nucleotide Sequencing -- Methods
  • Sequence Analysis, DNA -- Methods
ispartof: Nature biotechnology, April 2018, Vol.36(4), pp.338-345
description: 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.
language: eng
source:
identifier: E-ISSN: 1546-1696 ; PMID: 29431738 Version:1 ; DOI: 10.1038/nbt.4060
fulltext: fulltext
issn:
  • 15461696
  • 1546-1696
url: Link


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titleNanopore sequencing and assembly of a human genome with ultra-long reads
creatorJain, Miten ; Koren, Sergey ; Miga, Karen H ; Quick, Josh ; Rand, Arthur C ; Sasani, Thomas A ; Tyson, John R ; Beggs, Andrew D ; Dilthey, Alexander T ; Fiddes, Ian T ; Malla, Sunir ; Marriott, Hannah ; Nieto, Tom ; O'Grady, Justin ; Olsen, Hugh E ; Pedersen, Brent S ; Rhie, Arang ; Richardson, Hollian ; Quinlan, Aaron R ; Snutch, Terrance P ; Tee, Louise ; Paten, Benedict ; Phillippy, Adam M ; Simpson, Jared T ; Loman, Nicholas J ; Loose, Matthew
ispartofNature biotechnology, April 2018, Vol.36(4), pp.338-345
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subjectGenomics ; Genome, Human -- Genetics ; High-Throughput Nucleotide Sequencing -- Methods ; Sequence Analysis, DNA -- Methods
descriptionWe 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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titleNanopore sequencing and assembly of a human genome with ultra-long reads
descriptionWe 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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abstractWe 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.
doi10.1038/nbt.4060
pmid29431738
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date2018-04