Nanopore sequencing and assembly of a human genome with ultra-long reads
Nanopore sequencing and assembly of a human genome with ultra-long reads
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.
Rhie A、Quinlan AR、Tee L、Paten B、Loman NJ、Jain Miten、Quick J、Sasani TA、Beggs AD、Nieto T、Pedersen BS、Koren S、Rand AC、Loose M、Richardson H、Phillippy AM、Miga KH、O?ˉGrady J、Fiddes IT、Simpson JT、Snutch TP、Olsen HE、Tyson JR、Dilthey AT、Marriott H、Malla S
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research InstituteDepartment of Human Genetics, University of Utah||USTAR Center for Genetic Discovery, University of Utah||Department of Biomedical Informatics, University of UtahSurgical Research Laboratory, Institute of Cancer & Genomic Science, University of BirminghamUC Santa Cruz Genomics Institute, University of CaliforniaInstitute of Microbiology and Infection, University of BirminghamUC Santa Cruz Genomics Institute, University of CaliforniaInstitute of Microbiology and Infection, University of BirminghamDepartment of Human Genetics, University of Utah||USTAR Center for Genetic Discovery, University of UtahSurgical Research Laboratory, Institute of Cancer & Genomic Science, University of BirminghamSurgical Research Laboratory, Institute of Cancer & Genomic Science, University of BirminghamDepartment of Human Genetics, University of Utah||USTAR Center for Genetic Discovery, University of UtahGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research InstituteUC Santa Cruz Genomics Institute, University of CaliforniaDeepSeq, School of Life Sciences, University of NottinghamNorwich Medical School, University of East AngliaGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research InstituteUC Santa Cruz Genomics Institute, University of CaliforniaNorwich Medical School, University of East AngliaUC Santa Cruz Genomics Institute, University of CaliforniaOntario Institute for Cancer Research||Department of Computer Science, University of TorontoMichael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaUC Santa Cruz Genomics Institute, University of CaliforniaMichael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research InstituteDeepSeq, School of Life Sciences, University of NottinghamDeepSeq, School of Life Sciences, University of Nottingham
生物科学研究方法、生物科学研究技术遗传学分子生物学
Rhie A,Quinlan AR,Tee L,Paten B,Loman NJ,Jain Miten,Quick J,Sasani TA,Beggs AD,Nieto T,Pedersen BS,Koren S,Rand AC,Loose M,Richardson H,Phillippy AM,Miga KH,O?ˉGrady J,Fiddes IT,Simpson JT,Snutch TP,Olsen HE,Tyson JR,Dilthey AT,Marriott H,Malla S.Nanopore sequencing and assembly of a human genome with ultra-long reads[EB/OL].(2025-03-28)[2025-04-27].https://www.biorxiv.org/content/10.1101/128835.点此复制
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