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Typical Virome Analysis Workflows

Last Updated: November 29, 2025

This page outlines common workflows for virome analysis, showcasing how different tools from the Awesome-Virome collection can be combined to achieve specific research goals.

Important Note on Workflows

These workflows represent common approaches but should be adapted to your specific research questions and sample types. Always validate results and consider running multiple tools for critical analyses.

Basic Virome Analysis Workflow

For general metagenomic virome analysis, this basic workflow provides a solid foundation:

Raw Sequencing Data
→
Quality Control
→
Assembly
→
Viral Contig Identification
Functional Annotation
←
Host Prediction
←
Taxonomic Classification
←
Quality Assessment

Step-by-Step Guide

  1. Quality Control of Metagenomic Reads
    • Tools: Standard bioinformatics QC tools (Trimmomatic, FastQC, etc.)
    • Purpose: Remove low-quality reads, adapters, and contaminants
  2. Assembly of Contigs
    • Tools: SPAdes, MEGAHIT
    • Purpose: Assemble short reads into longer contiguous sequences (contigs)
  3. Identification of Viral Contigs
    • Tools: VirSorter2, VIBRANT, geNomad
    • Purpose: Identify which contigs are of viral origin
  4. Quality Assessment
    • Tools: CheckV
    • Purpose: Assess the completeness and quality of viral genomes
  5. Taxonomic Classification
    • Tools: vConTACT2, PhaGCN
    • Purpose: Assign taxonomy to viral sequences
  6. Host Prediction
    • Tools: iPHoP, CHERRY
    • Purpose: Predict the bacterial hosts of phages
  7. Functional Annotation
    • Tools: Pharokka, DRAMv
    • Purpose: Annotate genes and predict functions

RNA Virus Discovery Workflow

For specifically focusing on RNA viruses in your samples:

Raw RNA-Seq Data
→
Quality Control
→
Assembly
→
RdRp Search
Phylogenetic Analysis
←
Genome Annotation
←
RNA Virus Verification

Key Tools for RNA Virus Analysis

  1. RNA Virus Detection
    • Tools: palmID, RdRp-scan, metaviralSPAdes-RNA
    • Purpose: Identify RNA virus sequences by detecting conserved RdRp domains
  2. RNA Virus Annotation
    • Tools: VirMine-RNA
    • Purpose: Functional annotation specific to RNA viral genomes

Prophage Identification Workflow

For identifying integrated prophages in bacterial genomes:

Bacterial Genome
→
Prophage Detection
→
Prophage Excision
Host-Prophage Interaction Analysis
←
Prophage Annotation
←
Prophage Verification

Key Tools for Prophage Analysis

  1. Prophage Detection
    • Tools: PhiSpy, Phigaro, PHASTER
    • Purpose: Identify integrated viral sequences within bacterial genomes
  2. Prophage Analysis
    • Tools: viralintegration, hafeZ
    • Purpose: Analyze integration sites and characterize prophage regions

Advanced Workflows

These more specialized workflows address specific research questions:

Viral Quasispecies Analysis

For analyzing viral population diversity within a sample:

  1. Strain Reconstruction
    • Tools: VStrains, COBRA
    • Purpose: Reconstruct individual viral strains from complex metagenomic samples
  2. Quasispecies Analysis
    • Tools: ShoRAH, CliqueSNV
    • Purpose: Analyze genetic variation and population dynamics within viral communities

Virome-Host Interaction Analysis

For studying how viruses interact with their hosts:

  1. CRISPR Analysis
    • Tools: SpacePHARER, CrisprOpenDB
    • Purpose: Identify CRISPR spacers and predict virus-host relationships
  2. Protein-Protein Interactions
    • Tools: DeepVHPPI
    • Purpose: Predict interactions between viral and host proteins

For newcomers to virome analysis, here are some recommended starting points:

  1. Viral identification
    • Tools: VirSorter2, VIBRANT, geNomad
    • Difficulty: Beginner to Intermediate
    • Computational requirements: Moderate
  2. Host prediction
    • Tools: iPHoP, CHERRY
    • Difficulty: Intermediate
    • Computational requirements: Moderate to High
  3. Genome annotation
    • Tools: Pharokka, DRAMv
    • Difficulty: Beginner
    • Computational requirements: Low to Moderate
  4. Taxonomy assignment
    • Tools: vConTACT2, PhaGCN
    • Difficulty: Intermediate
    • Computational requirements: Moderate
  5. Quality control
    • Tools: CheckV
    • Difficulty: Beginner
    • Computational requirements: Low

Next Steps

  1. Explore Tools
    • Visit the Tools Overview section for detailed information about each tool
    • Check the Selection Guide to find the best tools for your specific needs
  2. Learn About Data Access
    • Review the API Reference to learn how to access the Awesome-Virome database programmatically
    • See API Examples for code snippets in Python, R, and JavaScript
  3. Join the Community