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.

中文翻译：

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具有超长读长的人类基因组的纳米孔测序和组装。


我们报告了使用 MinION (Oxford Nanopore Technologies) 纳米孔测序仪对人类 GM12878 Utah/Ceph 细胞系的参考基因组进行测序和组装。生成了 91.2 GB 的序列数据，代表~30×理论覆盖率。基于参考的比对能够检测大的结构变异和表观遗传修饰。纳米孔读数的从头组装单独产生了连续组装（NG50∼3 Mb）。我们开发了一种协议来生成超长读取（N50 > 100 kb，读取长度高达 882 kb）。对这些超长读段进行额外的 5 倍覆盖，使组装连续性增加了一倍以上 (NG50 ∼6.4 Mb)。最终组装的基因组大小为28.67亿个碱基，覆盖了参考的85.8%。合并互补短读长测序数据后，组装准确度超过 99.8%。超长读取能够实现 4 Mb 主要组织相容性复合体 (MHC) 基因座的整体组装和定相、端粒重复长度的测量以及参考人类基因组组装 GRCh38 中间隙的闭合。