RT Journal Article
SR Electronic
T1 Nanopore sequencing and assembly of a human genome with ultra-long reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 128835
DO 10.1101/128835
A1 Miten Jain
A1 S Koren
A1 J Quick
A1 AC Rand
A1 TA Sasani
A1 JR Tyson
A1 AD Beggs
A1 AT Dilthey
A1 IT Fiddes
A1 S Malla
A1 H Marriott
A1 KH Miga
A1 T Nieto
A1 J O’Grady
A1 HE Olsen
A1 BS Pedersen
A1 A Rhie
A1 H Richardson
A1 AR Quinlan
A1 TP Snutch
A1 L Tee
A1 B Paten
A1 AM Phillippy
A1 JT Simpson
A1 NJ Loman
A1 M Loose
YR 2017
UL http://biorxiv.org/content/early/2017/04/20/128835.abstract
AB Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. However until recently nanopore sequencing has been mainly applied to small genomes, due to the limited output attainable. We present nanopore sequencing and assembly of the GM12878 Utah/Ceph human reference genome generated using the Oxford Nanopore MinION and R9.4 version chemistry. We generated 91.2 Gb of sequence data (∼30× theoretical coverage) from 39 flowcells. De novo assembly yielded a highly complete and contiguous assembly (NG50 ∼3Mb). We observed considerable variability in homopolymeric tract resolution between different basecallers. The data permitted sensitive detection of both large structural variants and epigenetic modifications. Further we developed a new approach exploiting the long-read capability of this system and found that adding an additional 5×-coverage of ‘ultra-long’ reads (read N50 of 99.7kb) more than doubled the assembly contiguity. Modelling the repeat structure of the human genome predicts extraordinarily contiguous assemblies may be possible using nanopore reads alone. Portable de novo sequencing of human genomes may be important for rapid point-of-care diagnosis of rare genetic diseases and cancer, and monitoring of cancer progression. The complete dataset including raw signal is available as an Amazon Web Services Open Dataset at: https://github.com/nanopore-wgs-consortium/NA12878.