Nanopore sequencing and assembly of a human genome with ultra-long reads
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 la...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
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Nature Publishing Group
2018
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| Online Access: | https://eprints.nottingham.ac.uk/48665/ |
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| author | Jain, M. Koren, S. Miga, K.H. Quick, J. Rand, A.C. Sasani, T.A. Tyson, J.R. Beggs, A.D. Dilthey, A.T. Fiddes, I.T. Malla, S. Marriott, H. Nieto, T. O'Grady, J. Olsen, H.E. Pedersen, B.S. Rhie, A. Richardson, H. Quinlan, A.R. Snutch, T.P. Tee, L. Paten, B. Phillippy, A.M. Simpson, J.T. Loman, N.J. Loose, M. |
| author_facet | Jain, M. Koren, S. Miga, K.H. Quick, J. Rand, A.C. Sasani, T.A. Tyson, J.R. Beggs, A.D. Dilthey, A.T. Fiddes, I.T. Malla, S. Marriott, H. Nieto, T. O'Grady, J. Olsen, H.E. Pedersen, B.S. Rhie, A. Richardson, H. Quinlan, A.R. Snutch, T.P. Tee, L. Paten, B. Phillippy, A.M. Simpson, J.T. Loman, N.J. Loose, M. |
| author_sort | Jain, M. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data 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. |
| first_indexed | 2025-11-14T20:09:56Z |
| format | Article |
| id | nottingham-48665 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T20:09:56Z |
| publishDate | 2018 |
| publisher | Nature Publishing Group |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-486652020-05-04T19:28:34Z https://eprints.nottingham.ac.uk/48665/ Nanopore sequencing and assembly of a human genome with ultra-long reads Jain, M. Koren, S. Miga, K.H. Quick, J. Rand, A.C. Sasani, T.A. Tyson, J.R. Beggs, A.D. Dilthey, A.T. Fiddes, I.T. Malla, S. Marriott, H. Nieto, T. O'Grady, J. Olsen, H.E. Pedersen, B.S. Rhie, A. Richardson, H. Quinlan, A.R. Snutch, T.P. Tee, L. Paten, B. Phillippy, A.M. Simpson, J.T. Loman, N.J. Loose, M. 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). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data 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. Nature Publishing Group 2018-01-29 Article PeerReviewed Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H.E., Pedersen, B.S., Rhie, A., Richardson, H., Quinlan, A.R., Snutch, T.P., Tee, L., Paten, B., Phillippy, A.M., Simpson, J.T., Loman, N.J. and Loose, M. (2018) Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology . ISSN 1546-1696 https://www.nature.com/articles/nbt.4060 doi:10.1038/nbt.4060 doi:10.1038/nbt.4060 |
| spellingShingle | Jain, M. Koren, S. Miga, K.H. Quick, J. Rand, A.C. Sasani, T.A. Tyson, J.R. Beggs, A.D. Dilthey, A.T. Fiddes, I.T. Malla, S. Marriott, H. Nieto, T. O'Grady, J. Olsen, H.E. Pedersen, B.S. Rhie, A. Richardson, H. Quinlan, A.R. Snutch, T.P. Tee, L. Paten, B. Phillippy, A.M. Simpson, J.T. Loman, N.J. Loose, M. Nanopore sequencing and assembly of a human genome with ultra-long reads |
| title | Nanopore sequencing and assembly of a human genome with ultra-long reads |
| title_full | Nanopore sequencing and assembly of a human genome with ultra-long reads |
| title_fullStr | Nanopore sequencing and assembly of a human genome with ultra-long reads |
| title_full_unstemmed | Nanopore sequencing and assembly of a human genome with ultra-long reads |
| title_short | Nanopore sequencing and assembly of a human genome with ultra-long reads |
| title_sort | nanopore sequencing and assembly of a human genome with ultra-long reads |
| url | https://eprints.nottingham.ac.uk/48665/ https://eprints.nottingham.ac.uk/48665/ https://eprints.nottingham.ac.uk/48665/ |