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

Keylie M Gibson¹, Margaret C Steiner¹, Uzma Rentia¹

¹Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA.

|July 18, 2020

Summary

HAPHPIPE is a new bioinformatics tool that analyzes viral next-generation sequencing data. It accurately reconstructs viral consensus sequences and quantifies intra-host diversity, outperforming existing software.

Keywords:

HCV HIV SARS-CoV-2 bioinformatics consensus haplotypes simulation validation viruses

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Last Updated: Dec 14, 2025

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Published on: July 27, 2018

Area of Science:

Virology
Bioinformatics
Genomics

Background:

Next-generation sequencing (NGS) enables detection of low-abundance viral variants.
Current bioinformatics tools often prioritize consensus sequences, limiting intra-host diversity analysis.
Analyzing intra-host viral diversity is crucial for understanding viral evolution and disease dynamics.

Purpose of the Study:

To develop HAPHPIPE, an open-source tool for viral NGS data analysis.
To enable both consensus sequence assembly and intra-host variation quantification via haplotype reconstruction.
To provide a user-friendly platform for viral NGS assembly.

Main Methods:

HAPHPIPE was developed for de novo and reference-based assembly of viral NGS data.
Consensus sequence assembly methods were validated against HyDRA and Geneious using simulated and empirical HIV, HCV, and SARS-CoV-2 data.
Validation metrics included read mapping, genetic distance, and genetic diversity.

Main Results:

HAPHPIPE generated more accurate consensus sequences for HIV pol genes in simulated data compared to HyDRA and Geneious.
HAPHPIPE demonstrated comparable performance to Geneious for HIV gp120 sequences.
HAPHPIPE exhibited superior computational speed, enabling analysis of larger viral sequence datasets.

Conclusions:

HAPHPIPE offers improved accuracy and speed for viral NGS data assembly.
The tool facilitates comprehensive analysis of viral consensus sequences and intra-host diversity.
HAPHPIPE provides a user-friendly solution for researchers with varying bioinformatics expertise.