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

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Anton EliseevKeith A Crandall

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 viral populations simulated under realistic evolutionary dynamics. We simulated coalescent-based populations that spanned known levels of viral genetic diversity, including mutation rates, sample size and effective population size, to test the limits of the haplotype reconstruction methods and to ensure coverage of predicted intra-host viral diversity levels (especially HIV-1). All twelve investigated haplotype callers showed variable perform...Continue Reading

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Citations

May 23, 2020·Viruses·Margaret C SteinerKeith A Crandall
Dec 29, 2020·Molecular Biology and Evolution·Matthew L BendallKeith A Crandall
Jan 21, 2021·Bioinformatics·Susana Posada-CéspedesNiko Beerenwinkel
Apr 14, 2021·Nucleic Acids Research·Christian M GallardoBruce E Torbett
Jun 22, 2021·Current Opinion in Virology·Lara FuhrmannNiko Beerenwinkel
Jun 15, 2021·Interface Focus·Amanda Araújo Serrão de AndradeAna Tereza Ribeiro de Vasconcelos
Jun 23, 2020·Briefings in Bioinformatics·Sergey KnyazevAlexander Zelikovsky

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