Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies.

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 illustrate HaROLD on both RNA and DNA viruses with synthetic Illumina paired read data created from mixed human cytomegalov

SUBMITTER: Venturini C 

PROVIDER: S-EPMC9719071 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature