RT Journal Article
SR Electronic
T1 Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 519025
DO 10.1101/519025
A1 Aaron M. Wenger
A1 Paul Peluso
A1 William J. Rowell
A1 Pi-Chuan Chang
A1 Richard J. Hall
A1 Gregory T. Concepcion
A1 Jana Ebler
A1 Arkarachai Fungtammasan
A1 Alexey Kolesnikov
A1 Nathan D. Olson
A1 Armin Töpfer
A1 Chen-Shan Chin
A1 Michael Alonge
A1 Medhat Mahmoud
A1 Yufeng Qian
A1 Adam M. Phillippy
A1 Michael C. Schatz
A1 Gene Myers
A1 Mark A. DePristo
A1 Jue Ruan
A1 Tobias Marschall
A1 Fritz J. Sedlazeck
A1 Justin M. Zook
A1 Heng Li
A1 Sergey Koren
A1 Andrew Carroll
A1 David R. Rank
A1 Michael W. Hunkapiller
YR 2019
UL http://biorxiv.org/content/early/2019/01/13/519025.abstract
AB The major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002/NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.