PAIVS

PAIVS predicts avian influenza virus (AIV) subtypes from Next-Generation Sequencing (NGS) data to enable detection and genomic characterization of highly pathogenic avian influenza (HPAI) strains, including hemagglutinin H5 and H7 subtypes.

Key Features:

• Pre-processing of NGS Data: Performs quality control and preparation of raw NGS reads for downstream analysis.
• Reference-Guided AIV Subtyping: Assigns AIV subtypes using alignment to reference genomes.
• De Novo Assembly: Reconstructs viral genomes from sequencing reads when references are unavailable or unsuitable.
• Variant Calling: Identifies genetic variants within AIV genomes to assess mutation patterns.
• BLAST Analysis: Uses BLAST (Basic Local Alignment Search Tool) to identify closest full-length sequences in databases for comparative analysis.
• Graphical Summary: Produces visual representations of analysis results for interpretation and reporting.

Scientific Applications:

• Epidemiological Surveillance: Enables accurate subtyping to monitor and track AIV outbreaks.
• HPAI Monitoring: Supports detection and characterization of H5 and H7 highly pathogenic avian influenza strains.
• Comparative Genomics and Strain Identification: Identifies closest database sequences and supports strain classification via BLAST and assembly data.
• Virus Evolution and Molecular Epidemiology: Facilitates analysis of variants and genome assemblies to study evolutionary dynamics.
• Vaccine and Antiviral Research: Provides genomic data and variant information to inform vaccine strain selection and antiviral development.

Methodology:

PAIVS performs NGS pre-processing, reference-guided subtyping, de novo assembly, variant calling, and BLAST-based sequence identification.