title: Phased diploid genome assembly with single-molecule real-time sequencing.
abstract: While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata, samples that have challenged short-read assembly approaches. The FALCON-based assemblies are substantially more contiguous and complete than alternate short- or long-read approaches. The phased diploid assembly enabled the study of haplotype structure and heterozygosities between homologous chromosomes, including the identification of widespread heterozygous structural variation within coding sequences.
authors.affiliation: Pacific Biosciences, Menlo Park, California, USA.
authors.forename: Chen-Shan
authors.identifier: http://orcid.org/0000-0003-4394-2455
authors.initials: CS
authors.lastname: Chin
authors.affiliation: Pacific Biosciences, Menlo Park, California, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Peluso
authors.affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Fritz J
authors.identifier: http://orcid.org/0000-0001-6040-2691
authors.initials: FJ
authors.lastname: Sedlazeck
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Maria
authors.initials: M
authors.lastname: Nattestad
authors.affiliation: Pacific Biosciences, Menlo Park, California, USA.
authors.forename: Gregory T
authors.initials: GT
authors.lastname: Concepcion
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Alicia
authors.initials: A
authors.lastname: Clum
authors.affiliation: Pacific Biosciences, Menlo Park, California, USA.
authors.forename: Christopher
authors.identifier: http://orcid.org/0000-0002-0601-3254
authors.initials: C
authors.lastname: Dunn
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.
authors.forename: Ronan
authors.initials: R
authors.lastname: O'Malley
authors.affiliation: Department of Viticulture and Enology, University of California Davis, Davis, California, USA.
authors.forename: Rosa
authors.initials: R
authors.lastname: Figueroa-Balderas
authors.affiliation: Department of Viticulture and Enology, University of California Davis, Davis, California, USA.
authors.forename: Abraham
authors.initials: A
authors.lastname: Morales-Cruz
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.
authors.forename: Grant R
authors.identifier: http://orcid.org/0000-0002-2374-4091
authors.initials: GR
authors.lastname: Cramer
authors.affiliation: Dipartimento di Biotecnologie, Universita' degli Studi di Verona, Verona, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.
authors.forename: Chongyuan
authors.initials: C
authors.lastname: Luo
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
authors.affiliation: Department of Viticulture and Enology, University of California Davis, Davis, California, USA.
authors.forename: Dario
authors.identifier: http://orcid.org/0000-0002-4858-1508
authors.initials: D
authors.lastname: Cantu
authors.affiliation: Pacific Biosciences, Menlo Park, California, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Rank
authors.affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.|Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.|Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001487:Basidiomycota / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D004171:Diploidy; D016681:Genome, Fungal / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D027843:Vitis / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D018744:DNA, Plant