@article {78,
	title = {Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.},
	journal = {Nat Biotechnol},
	volume = {37},
	year = {2019},
	month = {2019 Oct},
	pages = {1155-1162},
	abstract = {<p>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 {\textquoteright}genome in a bottle{\textquoteright} (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.</p>},
	issn = {1546-1696},
	doi = {10.1038/s41587-019-0217-9},
	author = {Wenger, Aaron M and Peluso, Paul and Rowell, William J and Chang, Pi-Chuan and Hall, Richard J and Concepcion, Gregory T and Ebler, Jana and Fungtammasan, Arkarachai and Kolesnikov, Alexey and Olson, Nathan D and T{\"o}pfer, Armin and Alonge, Michael and Mahmoud, Medhat and Qian, Yufeng and Chin, Chen-Shan and Phillippy, Adam M and Schatz, Michael C and Myers, Gene and DePristo, Mark A and Ruan, Jue and Marschall, Tobias and Sedlazeck, Fritz J and Zook, Justin M and Li, Heng and Koren, Sergey and Carroll, Andrew and Rank, David R and Hunkapiller, Michael W}
}
