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M Jain, S Koren, KH Miga, J Quick, AC Rand, TA Sasani, JR Tyson, AD Beggs, AT Dilthey, IT Fiddes, S Malla, H Marriott, 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 and M Loose
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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Concepts
The Assembly, Cell, Base pair, Genetics, Human genome, Gene, Major histocompatibility complex, DNA
MeSH headings
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