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Typical Virome Analysis Workflows

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.

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