QAP

QAP analyzes viral quasispecies sequencing data to identify, quantify, and characterize virus community composition from next-generation sequencing (NGS) and third-generation sequencing (TGS) datasets for studies of population structure relevant to pathogenesis and therapeutic responses.

Key Features:

• Virus OTU Definition: Defines virus Operational Taxonomic Units (OTUs) to enable quantitative ecological analysis of viral strains within communities.
• Comprehensive Analysis Capabilities: Performs analyses of viral quasispecies to link genetic variation with biological phenotypes observed in clinical settings.
• Support for NGS and TGS: Processes both next-generation sequencing (NGS) and third-generation sequencing (TGS) datasets to provide broad coverage and resolution of genetic diversity.
• Strain Identification and Quantification: Identifies and quantifies viral strains within communities from large-scale sequencing data.
• Visualization Tools: Produces visualizations for interpreting complex viral community datasets.

Scientific Applications:

• Quasispecies Characterization: Characterizes viral quasispecies diversity and population structure.
• Clinical Phenotype Association: Links viral population diversity to biological phenotypes and can inform treatment strategies and predict therapeutic outcomes.
• Evaluation on Key Viruses: Has been evaluated using sequencing data from hepatitis B virus (HBV), hepatitis C virus (HCV), influenza virus, and human immunodeficiency virus (HIV).

Methodology:

Processes large-scale sequencing data to identify and quantify viral strains using NGS and TGS and integrates virus OTU definitions into the analysis pipeline for ecological assessments.