VIGA

VIGA identifies and assembles eukaryotic viral genomes from next-generation sequencing (NGS) data to enable virome identification and genome reconstruction.

Key Features:

• Modular Architecture: Composed of four modules—Identification, Taxonomic Annotation, Assembly, and Novel Virus Discovery—each targeting a specific step in viral sequence processing.
  • Identification: Detects viral sequences within NGS datasets.
  • Taxonomic Annotation: Provides detailed taxonomic classification of identified viral sequences.
  • Assembly: Constructs complete viral genomes from sequencing reads.
  • Novel Virus Discovery: Facilitates detection of previously uncharacterized viruses.
• Integration with Third-Party Tools: Leverages BLAST, Trinity, MetaCompass, and RagTag to support virus identification and genome assembly.
• Performance Evaluation: Validated on simulated and real virome datasets, yielding more complete viral genome assemblies and improved strain-level reconstruction from metatranscriptomic and metagenomic data.

Scientific Applications:

• Virome Studies: Enables comprehensive identification and characterization of viral communities (viromes), including known viruses.
• Disease Research: Applied to metatranscriptomic data from the Human Microbiome Project to reveal distinct virome profiles associated with prediabetes, Crohn's disease, and ulcerative colitis.

Methodology:

The identification module scans sequencing reads for viral sequences, the taxonomic annotation module classifies identified sequences, the assembly module constructs viral genomes, and the novel virus discovery module aids in detecting previously uncharacterized viruses; VIGA integrates BLAST, Trinity, MetaCompass, and RagTag to support these steps.