2018/01/29 by Miten Jain, Sergey Koren, Karen H. Miga +23 · 1 citation
Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms #Chromosomal and Genetic Variations #Minion #Nanopore sequencing #Sequence assembly #Reference genome #Genome #Computational biology #Hybrid genome assembly #Nanopore #Biology #Human genome #DNA sequencer #Genomics #DNA sequencing #De novo transcriptome assembly #Genetics #Gene #Nanotechnology #Transcriptome
paper · pdf · doi:10.1038/nbt.4060
openalex publication_date 2018/01/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/08
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.