ViReMaShiny

ViReMaShiny visualizes and facilitates analysis of viral recombination events detected in next-generation sequencing (NGS) data to support interpretation of viral evolution and intrahost diversity.

Key Features:

• Recombination visualization: Generates visual representations of recombination events across viral genomes to characterize event distribution and frequency.
• Integration with ViReMa and BED format: Accepts BED-format output from ViReMa (Viral-Recombination-Mapper) for downstream visualization and analysis.
• Standardized NGS data handling: Provides a consistent framework for visualizing recombination events derived from NGS datasets.
• Support for recombination-derived products: Enables analysis relevant to chimeric viruses, structural variants, sub-genomic RNAs, and defective RNAs.

Scientific Applications:

• Viral evolution and adaptation studies: Facilitates interpretation of recombination contributions to viral evolutionary dynamics and adaptation.
• Characterization of recombinant and chimeric genomes: Supports identification and inspection of chimeric viruses and structural variants produced by recombination.
• Sub-genomic and defective RNA analysis: Assists in detecting and describing sub-genomic RNAs and defective RNAs arising from recombination.
• Intrahost diversity assessment: Enables analysis of recombination-driven diversity within infected hosts from NGS data.

Methodology:

Maps recombination events across viral genomes using data generated by NGS technologies and accepts BED-format outputs from ViReMa for visualization and analysis.