Nanopore sequencing and assembly of a human genome with ultra-long reads.
Nanopore sequencing and assembly of a human genome with ultra-long reads.
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DOI：
10.1038/nbt.4060
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发表时间：
2018-04
影响因子：
46.9
通讯作者：
Loose M
中科院分区：
文献类型：
--
作者：
Jain M;Koren S;Miga KH;Quick J;Rand AC;Sasani TA;Tyson JR;Beggs AD;Dilthey AT;Fiddes IT;Malla S;Marriott H;Nieto T;O'Grady J;Olsen HE;Pedersen BS;Rhie A;Richardson H;Quinlan AR;Snutch TP;Tee L;Paten B;Phillippy AM;Simpson JT;Loman NJ;Loose M
使用袖珍纳米孔装置对人类基因组进行测序和从头组装。本文的在线版本（doi：10.1038/nbt.4060）包含补充材料，可供授权用户使用。我们报告了使用MinION（Oxford Nanopore Technologies）纳米孔测序仪对人GM 12878犹他州/Ceph细胞系的参考基因组的测序和组装。91.2产生了代表1030 ×理论覆盖率的Gb序列数据。基于参考的比对使得能够检测大的结构变体和表观遗传修饰。单独的纳米孔读数的从头组装产生连续组装（NG 50 ~ 3 Mb）。我们开发了一种产生超长读段（N50 > 100 kb，读段长度高达882 kb）的方案。将这些超长读段的额外5倍覆盖率增加一倍以上，使组装邻接度（NG 50 = 6.4 Mb）增加一倍以上。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%。在结合互补短读段测序数据后，组装准确率超过99.8%。超长读段使得能够组装和定相4-Mb主要组织相容性复合体（MHC）基因座的整体，测量端粒重复长度，以及闭合参考人类基因组组装GRCh 38中的缺口。本文的在线版本（doi：10.1038/nbt.4060）包含补充材料，可供授权用户使用。
A human genome is sequenced and assembled de novo using a pocket-sized nanopore device. The online version of this article (doi:10.1038/nbt.4060) contains supplementary material, which is available to authorized users. 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. The online version of this article (doi:10.1038/nbt.4060) contains supplementary material, which is available to authorized users.
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DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
3.7
作者：
Chen, YT;Iseli, C;Jongeneel, CV
通讯作者：
Jongeneel, CV
影响因子：
7
作者：
Eberle, Michael A.;Fritzilas, Epameinondas;Bentley, David R.
通讯作者：
Bentley, David R.
影响因子：
12.3
作者：
Jain M;Olsen HE;Paten B;Akeson M
通讯作者：
Akeson M