Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/116539
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Type: Journal article
Title: De novo assembly of haplotype-resolved genomes with trio binning
Author: Koren, S.
Rhie, A.
Walenz, B.P.
Dilthey, A.T.
Bickhart, D.M.
Kingan, S.B.
Hiendleder, S.
Williams, J.L.
Smith, T.P.
Phillippy, A.M.
Citation: Nature biotechnology, 2018; 36(12):1174-1182
Publisher: Springer
Issue Date: 2018
ISSN: 1087-0156
1546-1696
Statement of
Responsibility: 
Sergey Koren, Arang Rhie, Brian P Walenz, Alexander T Dilthey, Derek M Bickhart, Sarah B Kingan, Stefan Hiendleder, John L Williams, Timothy P L Smith, Adam M Phillippy
Abstract: Complex allelic variation hampers the assembly of haplotype-resolved sequences from diploid genomes. We developed trio binning, an approach that simplifies haplotype assembly by resolving allelic variation before assembly. In contrast with prior approaches, the effectiveness of our method improved with increasing heterozygosity. Trio binning uses short reads from two parental genomes to first partition long reads from an offspring into haplotype-specific sets. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. We used trio binning to recover both haplotypes of a diploid human genome and identified complex structural variants missed by alternative approaches. We sequenced an F1 cross between the cattle subspecies Bos taurus taurus and Bos taurus indicus and completely assembled both parental haplotypes with NG50 haplotig sizes of >20 Mb and 99.998% accuracy, surpassing the quality of current cattle reference genomes. We suggest that trio binning improves diploid genome assembly and will facilitate new studies of haplotype variation and inheritance.
Keywords: Genome assembly algorithms; genomics; haplotypes; sequencing
Rights: © 2018, Springer Nature
RMID: 0030100484
DOI: 10.1038/nbt.4277
Appears in Collections:Animal and Veterinary Sciences publications

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