Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

• Published in: PloS one Vol. 11; no. 1; p. e0147229
• Main Authors: Stapleton, James A, Kim, Jeongwoon, Hamilton, John P, Wu, Ming, Irber, Luiz C, Maddamsetti, Rohan, Briney, Bryan, Newton, Linsey, Burton, Dennis R, Brown, C Titus, Chan, Christina, Buell, C Robin, Whitehead, Timothy A
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20-01-2016; Public Library of Science (PLoS)
• Subjects: Algorithms; Animals; Bacteria; Bioinformatics; Cancer; Chromosomes; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Bacterial - genetics; DNA, Neoplasm - genetics; DNA, Plant - genetics; E coli; Env gene; Gene Library; Gene sequencing; Genetic aspects; Genome; Genomes; Genomics; Haplotypes; Haplotypes - genetics; High-Throughput Nucleotide Sequencing - methods; Humans; Methods; Molecular biology; mRNA; Multiplexing; Nucleic acids; Ribosomal DNA; Sequence Analysis, DNA - methods; Tumor cell lines; United States
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0147229

Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences from human cancer cell lines, and individual HIV env gene variants from a mixture. The preparation of multiple samples can be multiplexed into a single tube, further reducing effort and cost relative to competing approaches. Our approach generates sequencing libraries in three days from less than one microgram of DNA in a single-tube format without custom equipment or specialized expertise.