Title |
Nanopore sequencing and assembly of a human genome with ultra-long reads
|
---|---|
Published in |
Nature Biotechnology, January 2018
|
DOI | 10.1038/nbt.4060 |
Pubmed ID | |
Authors |
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Tom Nieto, Justin O'Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron R Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M Phillippy, Jared T Simpson, Nicholas J Loman, Matthew 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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 392 | 19% |
United Kingdom | 220 | 11% |
Canada | 62 | 3% |
Germany | 52 | 3% |
Australia | 46 | 2% |
France | 45 | 2% |
Spain | 44 | 2% |
Italy | 42 | 2% |
India | 39 | 2% |
Other | 325 | 16% |
Unknown | 812 | 39% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 1401 | 67% |
Scientists | 573 | 28% |
Practitioners (doctors, other healthcare professionals) | 63 | 3% |
Science communicators (journalists, bloggers, editors) | 41 | 2% |
Unknown | 1 | <1% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Japan | 1 | <1% |
United States | 1 | <1% |
Switzerland | 1 | <1% |
Unknown | 2378 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 471 | 20% |
Researcher | 415 | 17% |
Student > Master | 282 | 12% |
Student > Bachelor | 274 | 12% |
Other | 99 | 4% |
Other | 353 | 15% |
Unknown | 487 | 20% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 775 | 33% |
Agricultural and Biological Sciences | 498 | 21% |
Computer Science | 117 | 5% |
Medicine and Dentistry | 74 | 3% |
Engineering | 70 | 3% |
Other | 292 | 12% |
Unknown | 555 | 23% |