Nanopore sequencing and assembly of a human genome with ultra-long reads
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Abstract
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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The record
- Venue
- Nature Biotechnology
- Topic
- Genomics and Phylogenetic Studies
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- University of TorontoOntario Institute for Cancer ResearchMichael Smith Health Research BCUniversity of British Columbia
- Funders
- National Cancer InstituteBiotechnology and Biological Sciences Research CouncilMedical Research CouncilCanadian Institutes of Health ResearchMichael Smith Health Research BCSurgical Reconstruction and Microbiology Research CentreRosetrees TrustNational Institute of General Medical SciencesNational Institute for Health and Care ResearchGenome British ColumbiaNational Institutes of HealthCancer Research UKNational Human Genome Research InstituteWellcome TrustOntario Institute for Cancer ResearchGovernment of CanadaFondation Brain Canada
- Keywords
- MinionNanopore sequencingSequence assemblyReference genomeGenomeComputational biologyHybrid genome assemblyNanoporeBiologyHuman genomeDNA sequencerGenomicsDNA sequencingDe novo transcriptome assemblyGeneticsGeneNanotechnologyTranscriptome
- Has abstract in OpenAlex
- yes