![]() ![]() Even more challenging are the pericentromeric, centromeric, and acrocentric short arms of chromosomes, which contain satellite DNA and tandem repeats of 3–10 Mb in length 7, 8. This is due to size ( ∼3.1 Gb), heterozygosity, regions of GC% bias, diverse repeat families, and segmental duplications (up to 1.7 Mbp in size) that make up at least 50% of the genome 6. Despite improvements in sequencing technology, assembling human genomes with high accuracy and completeness remains challenging. The human genome is used as a yardstick to assess performance of DNA sequencing instruments 1, 2, 3, 4, 5. ![]() 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. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Incorporating an additional 5× coverage of these ultra-long reads more than doubled the assembly contiguity (NG50 ∼6.4 Mb). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb). De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ∼3 Mb). Reference-based alignment enabled detection of large structural variants and epigenetic modifications. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. 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. Nature Biotechnology volume 36, pages 338–345 ( 2018) Cite this article Nanopore sequencing and assembly of a human genome with ultra-long reads ![]()
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