TY - JOUR T1 - Haplotype assignment of virus NGS data using co-variation of variant frequencies JF - bioRxiv DO - 10.1101/444877 SP - 444877 AU - Richard A. Goldstein AU - Asif U. Tamuri AU - Sunando Roy AU - Judith Breuer Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/10/17/444877.abstract N2 - 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 to identify 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 describe a new approach to perform this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We test this method with data sets of mixed cytomegalovirus genomes, demonstrating high accuracy when longitudinal samples are available. ER -