ViQuaS

ViQuaS reconstructs viral quasispecies spectra from short next-generation sequencing reads to characterize intra-host viral diversity in RNA viruses and some DNA viruses for studies of viral evolution, drug resistance, and vaccine design.

Key Features:

• Reference-Assisted De Novo Assembly Algorithm: Employs a reference-assisted de novo assembly algorithm to construct local haplotypes from short next-generation sequencing reads.
• Extended Global Strain Reconstruction Algorithm: Incorporates an extended global strain reconstruction algorithm to assemble complete strain sequences.
• Performance Benchmarking: Benchmarked against ShoRAH, QuRe, and PredictHaplo with reported improvements in recall (3.1–53.9%), precision (0–12.1%), F-score (0–38.2%), KL-divergence (improvement 0.006–0.143), and root-mean-squared error (improvement 0.001–0.035) for strain sequence assembly and frequency estimation.
• Application to Real Datasets: Applied to an in vitro human immunodeficiency virus (HIV)-1 population, two independent foot-and-mouth disease virus datasets from the same biological sample, and a real HIV-1 dataset, where it outperformed other methods.

Scientific Applications:

• Viral genetic diversity analysis: Provides reconstructed strain sequences and frequency estimates to characterize genetic diversity in RNA viruses and some DNA viruses.
• Viral evolution studies: Enables analysis of viral evolution and intra-host dynamics using reconstructed haplotypes and strain frequencies.
• Resistance mechanism investigation: Supports investigation of antiviral resistance mechanisms by resolving minority variants and strain frequencies.
• Antiviral and vaccine design support: Informs antiviral drug and vaccine design through accurate strain sequence assembly and frequency estimation.
• Clinical and research viral dynamics analysis: Facilitates analyses of viral dynamics in both clinical and research samples.

Methodology:

Uses a reference-assisted de novo assembly algorithm to construct local haplotypes and an extended global strain reconstruction algorithm to assemble global strains from short next-generation sequencing reads.