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bioRxiv · 10.1101/444877

Haplotype assignment of virus NGS data using co-variation of variant frequencies

Goldstein, R. A.·Tamuri, A. U.·Roy, S.·Breuer, J.
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Abstract

Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We test this method with synthetic data sets of mixed cytomegalovirus and norovirus genomes, demonstrating high accuracy when longitudinal samples are available.

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Goldstein, R. A., Tamuri, A. U., Roy, S., Breuer, J.. 2018-10-17. Haplotype assignment of virus NGS data using co-variation of variant frequencies. https://doi.org/10.1101/444877

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