Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated
Gibson, K. M., Steiner, M. C., Rentia, U., Bendall, M. L., Pérez-Losada, M., & Crandall, K. A. (2020). Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.. Viruses, 12 (7). http://dx.doi.org/10.3390/v12070758