title: Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.
abstract: 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.
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: James A
authors.initials: JA
authors.lastname: Stapleton
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Jeongwoon
authors.initials: J
authors.lastname: Kim
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: John P
authors.initials: JP
authors.lastname: Hamilton
authors.affiliation: Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, 48109, United States of America.
authors.forename: Ming
authors.initials: M
authors.lastname: Wu
authors.affiliation: Department of Microbiology and Molecular Genetics and Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Luiz C
authors.initials: LC
authors.lastname: Irber
authors.affiliation: BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America.|Department of Integrative Biology, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Rohan
authors.initials: R
authors.lastname: Maddamsetti
authors.affiliation: Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America.|Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America.|International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America.
authors.forename: Bryan
authors.initials: B
authors.lastname: Briney
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Linsey
authors.initials: L
authors.lastname: Newton
authors.affiliation: Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America.|Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America.|International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America.
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Burton
authors.affiliation: Department of Microbiology and Molecular Genetics and Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America.|Population Health and Reproduction, University of California Davis, Davis, California, United States of America.
authors.forename: C Titus
authors.initials: CT
authors.lastname: Brown
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Christina
authors.initials: C
authors.lastname: Chan
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America.|Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Whitehead
mesh_terms: D000465:Algorithms; D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D016678:Genome; D006239:Haplotypes / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D004273:DNA, Neoplasm; D018744:DNA, Plant