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Virome Analysis Tutorials

Last Updated: November 29, 2025

Welcome to the Awesome-Virome tutorial collection. These hands-on tutorials guide you through complete virome analysis workflows, from raw sequencing data to publication-ready results.

Tutorial Overview

Each tutorial includes: - Complete workflows with all commands and parameters - Test datasets that you can download and analyze - Expected outputs at each step for validation - Troubleshooting for common issues - Interpretation guides to understand your results

Available Tutorials

1. Basic Metagenome Virome Analysis

Level: Beginner | Time: 4-6 hours | Data: 50MB test dataset

Learn the fundamental workflow for discovering viruses in metagenomic data.

  • Quality control of raw sequencing reads
  • Assembly strategies for viral metagenomes
  • Viral sequence identification with multiple tools
  • Quality assessment and validation
  • Taxonomic classification
  • Abundance estimation

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2. RNA Virus Discovery

Level: Intermediate | Time: 6-8 hours | Data: 100MB test dataset

Discover RNA viruses in transcriptomic or metagenomic data.

  • RNA extraction and library preparation considerations
  • Quality control for RNA-seq data
  • Assembly of RNA viral genomes
  • RdRp-based virus identification
  • RNA virus annotation
  • Phylogenetic placement

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3. Prophage Identification in Bacterial Genomes

Level: Intermediate | Time: 3-4 hours | Data: 20MB test dataset

Identify and characterize prophages integrated in bacterial genomes.

  • Working with bacterial isolate genomes
  • Multiple prophage prediction tools
  • Validation and quality assessment
  • Distinguishing active vs. cryptic prophages
  • Prophage excision and induction analysis
  • Comparative prophage genomics

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4. Comparative Virome Analysis

Level: Advanced | Time: 8-12 hours | Data: 500MB test dataset

Compare viral communities across multiple samples and conditions.

  • Experimental design for comparative studies
  • Batch processing multiple samples
  • Viral contig clustering and dereplication
  • Abundance normalization strategies
  • Statistical analysis of viral communities
  • Visualization and interpretation

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5. Host Prediction Workflows

Level: Advanced | Time: 6-10 hours | Data: 200MB test dataset

Predict bacterial hosts for newly discovered phages.

  • Multiple host prediction approaches
  • CRISPR spacer-based host assignment
  • Sequence homology methods
  • Machine learning-based predictions
  • Consensus approaches and validation
  • Integrating host prediction with microbiome data

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Before You Begin

Prerequisites

All tutorials assume you have:

  1. Basic command line skills - Familiarity with navigating directories, running commands
  2. Bioinformatics fundamentals - Understanding of FASTA/FASTQ formats, sequencing basics
  3. Computational resources - At minimum: 16GB RAM, 50GB disk space, 4 CPU cores

Software Installation

Most tutorials use tools available through Conda/Bioconda:

# Create a conda environment for virome analysis
conda create -n virome python=3.9
conda activate virome

# Install common tools (specific tools listed in each tutorial)
conda install -c bioconda -c conda-forge \
    fastp \
    spades \
    checkv \
    prodigal \
    blast \
    hmmer

Test Datasets

All tutorial datasets are hosted on Zenodo with DOIs for reproducibility:

Simulated Datasets

These tutorials use simulated/controlled datasets to ensure reproducible results and reasonable runtimes. Real-world data will have additional complexities, but the analytical approaches remain the same.

Learning Paths

Path 1: Complete Beginner

  1. Start with Tutorial 1 (Basic Metagenome Virome Analysis)
  2. Review Fundamentals for background concepts
  3. Move to Tutorial 3 (Prophage Identification) - simpler than Tutorial 2
  4. Tackle Tutorial 2 (RNA Virus Discovery)
  5. Advance to Tutorials 4 & 5 when confident

Path 2: Experience with Metagenomics

  1. Skim Tutorial 1 to understand virome-specific differences
  2. Jump to Tutorial 4 (Comparative Virome) for real-world scenarios
  3. Add Tutorial 5 (Host Prediction) for ecological insights
  4. Explore Tutorial 2 if working with RNA viruses

Path 3: Specific Research Focus

Gut microbiome researchers: - Tutorial 1 → Tutorial 3 → Tutorial 4 → Tutorial 5

Marine/environmental virologists: - Tutorial 1 → Tutorial 4 → Tutorial 5

Plant/RNA virologists: - Tutorial 2 → Tutorial 1 (for metagenomics background)

Bacterial genomics + phages: - Tutorial 3 → Tutorial 5 → Tutorial 1

Getting Help

Tutorial-Specific Issues

Each tutorial includes a troubleshooting section for common problems. Check there first.

General Questions

Community Support

Contributing Tutorials

Have a tutorial idea or improvement? We welcome contributions:

  1. Open a GitHub Issue describing your tutorial
  2. Follow our Contributing Guidelines
  3. Submit a pull request with your tutorial

Tutorial requirements: - Complete, tested workflow with all commands - Publicly available test dataset (<500MB) - Expected outputs and validation steps - Troubleshooting section - Estimated completion time

Next Steps

Ready to start? Choose your first tutorial from the list above, or review the Fundamentals section if you need more background.

Further Reading

Books

  • "Viral Ecology" by Christon J. Hurst (comprehensive virology background)
  • "Metagenomics: Methods and Protocols" (Methods in Molecular Biology series)

Review Papers

  • Roux, S., et al. (2019). "Minimum Information about an Uncultivated Virus Genome (MIUViG)." Nature Biotechnology, 37(1), 29-37.
  • Gregory, A. C., et al. (2019). "Marine DNA viral macro- and microdiversity from pole to pole." Cell, 177(5), 1109-1123.
  • Shkoporov, A. N., & Hill, C. (2019). "Bacteriophages of the human gut: the 'known unknown' of the microbiome." Cell Host & Microbe, 25(2), 195-209.

Online Courses