Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

Viruses
Keylie M GibsonKeith A Crandall

Abstract

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 pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to ...Continue Reading

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Citations

Dec 29, 2020·Molecular Biology and Evolution·Matthew L BendallKeith A Crandall

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Datasets Mentioned

BETA
PRJNA506879
SRR11140750

Methods Mentioned

BETA
Illumina sequencing

Software Mentioned

Bioconda
REGA HIV subtyping
PASeq
Viral
SPAdes
MiCall
HAPHPIPE
CLC Main Workbench
MountRainier
REGA

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