Dataset Information

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.

SUBMITTER: Chin CS

PROVIDER: S-EPMC5503144 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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

Chin Chen-Shan CS Peluso Paul P Sedlazeck Fritz J FJ Nattestad Maria M Concepcion Gregory T GT Clum Alicia A Dunn Christopher C O'Malley Ronan R Figueroa-Balderas Rosa R Morales-Cruz Abraham A Cramer Grant R GR Delledonne Massimo M Luo Chongyuan C Ecker Joseph R JR Cantu Dario D Rank David R DR Schatz Michael C MC

Nature methods 20161017 12

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 F ...[more]

PMID: 27749838

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Dataset Information

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

Publications

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

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