Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
Abstract
The major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We develop a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate, long reads and apply it to sequence the well-characterized human, HG002/NA24385, to 28-fold coverage with 13.5 kb CCS reads that average 99.5% accuracy. We apply existing tools to comprehensively detect variants, and achieve precision and recall above 99.9% for SNVs, 95.9% for indels, and 95.2% for structural variants. Nearly all (99.6%) 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 over Q45 (99.997%). From manual curation of discordances, we estimate 1,283 mistakes in the high-quality Genome in a Bottle benchmark are correctable with CCS reads. With only CCS reads, we match or exceed performance of variant detection with accurate short reads and assembly with noisy long reads.
Research Areas
