Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

Authors: Kronenberg, Zev N. and Rhie, Arang and Koren, Sergey and Concepcion, Gregory T. and Peluso, Paul and Munson, Katherine M. and Hiendleder, Stefan and Fedrigo, Olivier and Jarvis, Erich D. and Phillippy, Adam M. and Eichler, Evan E. and Williams, John L. and Smith, Tim P.L. and Hall, Richard J. and Sullivan, Shawn T. and Kingan, Sarah B.

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.

Journal: BioRxiv
DOI: 10.1101/327064
Year: 2019

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