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De novo assembly of haplotype-resolved genomes with trio binning

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.

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Figure 1: Outline of trio binning and haplotype assembly.
Figure 2: Effect of data characteristics on trio binning.
Figure 3: Read and assembly k-mer statistics for an Arabidopsis thaliana F1 hybrid.
Figure 4: Haplotype variation in a diploid human genome.
Figure 5: Diploid assembly of a Bos taurus F1 hybrid.

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Acknowledgements

We thank W, Thompson, K. Kuhn, K. McClure and R. Lee for technical assistance, and T. Graves-Lindsay and Washington University in St. Louis for public release of the PacBio NA12878 data. S.K., A.R., B.P.W. and A.M.P. were supported by the Intramural Research Program of the National Human Genome Research Institute, US National Institutes of Health. S.H. and J.L.W. were funded from the JS Davies bequest to the University of Adelaide. T.P.L.S. was supported by USDA-ARS Project 3040-31000-100-00D. D.M.B. was supported by USDA-ARS Project 5090-31000-026-00-D. This research was also supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI17C2098). This work used the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov).

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Contributions

A.M.P. and T.P.L.S. conceived and coordinated the project. S.K. and A.R. designed the trio-binning method. S.K., A.R. and B.P.W. implemented the software. S.K., A.R., B.P.W., A.T.D., D.M.B., S.B.K. and A.M.P. performed analyses. S.H. designed and performed breeding experiments and sample collections. J.L.W. contributed to development of the concept and provision of samples. T.P.L.S. performed sequencing. S.K., A.R., T.P.L.S., J.L.W. and A.M.P. wrote the manuscript. All of the authors approved the final manuscript.

Corresponding authors

Correspondence to Timothy P L Smith or Adam M Phillippy.

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S.B.K. is a current employee of Pacific Biosciences.

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Koren, S., Rhie, A., Walenz, B. et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat Biotechnol 36, 1174–1182 (2018). https://doi.org/10.1038/nbt.4277

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