Extended haplotype phasing of de novo genome assemblies with FALCON-Phase
Zev N. Kronenberg,
Gregory T. Concepcion,
Katherine M Munson,
Erich J Jarvis,
Evan E. Eichler,
John L. Williams,
Tim P.L. Smith,
Richard J Hall,
Shawn T Sullivan,
Sarah B. Kingan
Posted 21 May 2018
bioRxiv DOI: 10.1101/327064
Posted 21 May 2018
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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