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bioRxiv · 10.1101/327064

FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes

Kronenberg, Z. N.·Hall, R. J.·Hiendleder, S.·Smith, T. P. L.·Sullivan, S. T.·Williams, J. L.·Kingan, S. B.
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Abstract

Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. These assemblies can be created in various ways, such as use of tissues that contain single-haplotype (haploid) genomes, or by co-sequencing of parental genomes, but these approaches can be impractical in many situations. We present FALCON-Phase, which integrates long-read sequencing data and ultra-long-range Hi-C chromatin interaction data of a diploid individual to create high-quality, phased diploid genome assemblies. The method was evaluated by application to three datasets, including human, cattle, and zebra finch, for which high-quality, fully haplotype resolved assemblies were available for benchmarking. Phasing algorithm accuracy was affected by heterozygosity of the individual sequenced, with higher accuracy for cattle and zebra finch (>97%) compared to human (82%). In addition, scaffolding with the same Hi-C chromatin contact data resulted in phased chromosome-scale scaffolds.

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Kronenberg, Z. N., Hall, R. J., Hiendleder, S., Smith, T. P. L., Sullivan, S. T., Williams, J. L., Kingan, S. B.. 2018-05-21. FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes. https://doi.org/10.1101/327064

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