AccuVIR

AccuVIR assembles and polishes viral genomes from third-generation long-read sequencing data, leveraging viral gene structural properties to distinguish true genetic variants from Nanopore sequencing errors for RNA viruses such as Ebola, Zika, and SARS-CoV-2.

Key Features:

• Error Correction and Polishing: Distinguishes true genetic variants from sequencing errors by leveraging the high density of coding regions in RNA viruses and correcting errors that disrupt gene structures.
• Path Searching and Sampling: Employs path searching and sampling techniques within sequence alignment graphs to explore alternative sequence paths for assembly or polishing of draft viral genomes.
• Handling Long Reads: Optimized for long reads from third-generation sequencing technologies such as Nanopore, addressing high per-base error rates in real-time viral sequencing.

Scientific Applications:

• Virus Evolution Studies: Provides complete and accurate viral genomes to identify genetic variants that inform studies of viral adaptation and evolution.
• Genotype-Phenotype Relationships: Supports analysis linking viral genotypes to phenotypic properties such as transmissibility and virulence.
• Real-Time Surveillance: Enables accurate genome reconstruction from long-read sequencing data to support outbreak monitoring and real-time surveillance of emerging viral threats.

Methodology:

Performs path searching and sampling within sequence alignment graphs and evaluates candidate paths against known gene structures to filter sequencing errors that disrupt coding regions.