Vicuna

Vicuna assembles consensus genomes from ultra-deep sequencing data of genetically heterogeneous populations to enable accurate mapping of intra-host viral variants.

Key Features:

• De novo population consensus assembly: Constructs a single linear consensus representation from ultra-deep sequencing reads to serve as a reference for intra-host variant mapping.
• Handling genetic heterogeneity: Manages extensive genetic diversity, contaminants, and uneven sequence coverage to produce full-length genomes from heterogeneous populations.
• Robust variant mapping: Captures insertion/deletion polymorphisms and maintains high base-calling accuracy in final assemblies.
• Versatility across viral types: Demonstrated on Dengue, Human Immunodeficiency Virus (HIV), and West Nile virus populations with varying levels of intra-host diversity.
• Broad applicability: Applicable to other complex datasets such as metagenomic samples and tumor cell populations for consensus assembly of diverse mixtures.

Scientific Applications:

• Viral disease progression: Supports genetic studies of within-host viral evolution and disease progression by providing consensus assemblies and mapped variants.
• Transmission dynamics: Enables analysis of genetic variation across samples to inform transmission pattern inference.
• Viral evolution studies: Facilitates investigation of evolutionary patterns and mechanisms in viruses with extensive intra-host diversity.

Methodology:

Vicuna employs a de novo assembly algorithm tailored for ultra-deep sequencing data from heterogeneous populations to recover full-length consensus sequences and accurately represent genetic polymorphisms.