Journal
NATURE BIOTECHNOLOGY
Volume 37, Issue 10, Pages 1155-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41587-019-0217-9
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Funding
- National Human Genome Research Institute, National Institutes of Health
- NIH [1R01HG010040, UM1 HG008898]
- NSFC [31571353, 31822029]
- National Science Foundation [DBI-1350041]
- National Institutes of Health [R01-HG006677]
- German Research Foundation DFG) [391137747, 395192176]
- National Institute of Standards and Technology
- U.S. Food and Drug Administration
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [ZIAHG200398] Funding Source: NIH RePORTER
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The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.
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