Gene

Nanopore

Biology

Materials science

Minion

Reference genome

Nanopore sequencing

DNA sequencing

Sequence assembly

Computational biology

Hybrid genome assembly

Genetics

Transcriptome

Nanotechnology

Genome

Genomics

De novo transcriptome assembly

DNA sequencer

Gene expression

Human genome

Nature Biotechnology

A human genome is sequenced and assembled de novo using a pocket-sized nanopore device. 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.

Nanopore sequencing and assembly of a human genome with ultra-long reads