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Contributing to Awesome-Virome

Thank you for considering contributing to Awesome-Virome! This document provides guidelines and instructions for contributing to this curated list of virome analysis tools.

Ways to Contribute

There are several ways to contribute to Awesome-Virome:

  1. Add New Tools: Submit entries for tools not yet included in the list
  2. Update Information: Help keep tool descriptions and links up to date
  3. Report Issues: Let us know about broken links or outdated information
  4. Improve Documentation: Suggest enhancements to the documentation
  5. Fix Bugs: Help resolve issues with the website or dashboard

Contribution Process

Option 1: Submit an Issue

The easiest way to contribute is by submitting an issue:

  1. Go to the Issues page and click "New Issue"
  2. Select the appropriate template:
  3. Tool Addition: For suggesting new tools
  4. Tool Update: For updating existing tool information
  5. Bug Report: For reporting issues with the repository
  6. Feature Request: For suggesting new features
  7. Fill out all required fields
  8. Submit the issue

Our team will review your submission and incorporate valid contributions.

Option 2: Submit a Pull Request

For more direct contributions:

  1. Fork the repository
  2. Create a new branch for your addition (git checkout -b add-new-tool)
  3. Make your changes
  4. Submit a pull request

Guidelines for Tool Entries

Each tool entry should follow this format:

- [Tool Name](link-to-tool) - Brief description of the tool. [package-manager] [language]

Where: - Tool Name: The name of the software, tool, or database - link-to-tool: A URL to the tool's website, GitHub repository, or paper - Brief description: Explains what the tool does in 1-2 sentences - package-manager: Indicates how the tool can be installed (conda, pip, etc.) - language: Indicates the programming language used (optional)

Example:

- [ViralMSA](https://github.com/niemasd/ViralMSA) - Python script for viral multiple sequence alignment using read mappers. [source] [Python]

Detailed Requirements

Required Information

Every tool submission must include:

  1. Tool Name: The official name of the tool
  2. URL: A link to the tool's repository, website, or publication
  3. Description: A clear, concise description of what the tool does
  4. Category: The appropriate category for the tool

For higher quality entries, include:

  1. Version Information: The latest release version, if available
  2. Installation Method: How to install the tool (conda, pip, docker, etc.)
  3. Programming Language: The primary language the tool is written in
  4. License Information: The license under which the tool is distributed
  5. Citation Information: DOI or publication reference
  6. GitHub Stars: For GitHub repositories (automatically collected)
  7. Maintenance Status: Whether the tool is actively maintained

Quality Requirements

Your submission will be evaluated against these key criteria:

  1. Relevance: The tool must be relevant to virome analysis
  2. Accessibility: The URL must be accessible and correct
  3. Clarity: The description must be clear and informative
  4. Categorization: The tool must be placed in the correct category

Automated Validation

All submissions undergo automated validation:

  1. URLs are checked for accessibility
  2. Descriptions are analyzed for clarity and relevance
  3. Submissions are checked for duplicates
  4. DOIs and citations are validated when provided

A quality score (0-100) is assigned based on these checks. Submissions scoring below 70 require improvements before acceptance.

Enhanced Metadata Collection

For tools hosted on GitHub, GitLab, or Bitbucket, we automatically collect:

  • Repository statistics (stars, forks, open issues)
  • License information
  • Programming languages
  • Repository topics/tags
  • Release information
  • Creation and update dates

This metadata is updated weekly/monthly and used in our visualizations.

Code of Conduct

By participating in this project, you agree to abide by our Code of Conduct:

  • Be respectful and inclusive
  • Focus on the technical merits of submissions
  • Provide constructive feedback
  • Maintain a positive and helpful environment

Attribution

We appreciate all contributions to Awesome-Virome. Contributors are recognized in the following ways:

  • Listed in the Contributors section of the repository
  • Acknowledged in release notes for significant contributions
  • Credited in the changelog

Questions?

If you have questions about contributing, please:

  1. Check the FAQ
  2. Ask in GitHub Discussions
  3. Open an issue labeled "question"

Thank you for your contributions to the virome analysis community!