Phased diploid genome assembly with single-molecule real-time sequencing.

Authors: Chin, Chen-Shan and Peluso, Paul and Sedlazeck, Fritz J and Nattestad, Maria and Concepcion, Gregory T and Clum, Alicia and Dunn, Christopher and O'Malley, Ronan and Figueroa-Balderas, Rosa and Morales-Cruz, Abraham and Cramer, Grant R and Delledonne, Massimo and Luo, Chongyuan and Ecker, Joseph R and Cantu, Dario and Rank, David R and Schatz, Michael C

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.

Journal: Nature methods
DOI: 10.1038/nmeth.4035
Year: 2016

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