Evaluation of haplotype callers for next-generation sequencing of viruses.

ABSTRACT: Currently, the standard practice for assembling next-generation sequencing (NGS) reads of viral genomes is to summarize thousands of individual short reads into a single consensus sequence, thus confounding useful intra-host diversity information for molecular phylodynamic inference. It is hypothesized that a few viral strains may dominate the intra-host genetic diversity with a variety of lower frequency strains comprising the rest of the population. Several software tools currently exist to convert NGS sequence variants into haplotypes. Previous benchmarks of viral haplotype reconstruction programs used simulation scenarios that are useful from a mathematical perspective but do not reflect viral evolution and epidemiology. Here, we tested twelve NGS haplotype reconstruction methods using

SUBMITTER: Eliseev A 

PROVIDER: S-EPMC7293574 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature