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Introduction to Awesome-Virome

Welcome to the official documentation for Awesome-Virome, a curated list of software, tools, and databases useful for virome analysis, including phages, viruses, and their interactions with hosts.

What is Virome Analysis?

Virome analysis involves studying the collection of viruses (including bacteriophages) in a specific environment such as the human gut, soil, or oceans. These analyses typically include:

  1. Identifying viral sequences in metagenomic data
  2. Classifying viruses and predicting their hosts
  3. Assembling and annotating viral genomes
  4. Analyzing viral diversity and evolution
  5. Studying virus-host interactions and functional potential

How to Use This Documentation

This documentation is organized into several sections:

  • Getting Started: Basic information about virome analysis and how to use this repository
  • Tools: Detailed information about the tools included in Awesome-Virome
  • API Reference: Documentation for the programmatic API
  • Contributing: Guidelines for contributing to Awesome-Virome

You can navigate through the documentation using the navigation bar. If you're looking for a specific tool or topic, you can use the search function at the top of the page.

Key Features

Awesome-Virome offers several unique features that enhance its value as a resource for the viral bioinformatics community:

Interactive Visualizations

  • Dynamic network graph showing tool relationships and connections
  • Citation analytics with growth trends and impact metrics
  • Tool categorization treemap for understanding the ecosystem
  • Timeline visualization showing field development over time

Enhanced Metadata Collection

  • Automated metadata enrichment from GitHub, GitLab and Bitbucket
  • Detailed repository statistics including stars, forks, and languages
  • License information and release history tracking
  • Programming language distribution analysis

Community Contributions

  • Standardized issue templates for tool additions and updates
  • Automated workflows for data validation and site health checks
  • Detailed contribution guidelines for consistent data entry
  • Regular updates to ensure tool information remains current

Data Access Options

  • Web interface for browsing and searching tools
  • Interactive dashboard for visual exploration
  • RESTful API for programmatic access
  • Markdown files for simple text-based access

Ranked by GitHub stars:

  1. AlphaFold-Multimer - ⭐ 13320 stars
  2. CovidMD - ⭐ 2365 stars
  3. BLAST+DIAMOND - ⭐ 1114 stars
  4. coronaSPAdes - ⭐ 797 stars
  5. coronaSPAdes/metaviralSPAdes - ⭐ 797 stars

Next Steps

  • Check out the Typical Workflows page to learn how to use the tools in Awesome-Virome
  • Explore the Interactive Dashboard to visualize the tool ecosystem
  • Browse the Tools section to find tools for your specific needs