BioCheats: Bioinformatics Cheatsheets

Welcome to BioCheats, a repository of cheatsheets designed specifically for bioinformaticians working with command-line tools. This project offers quick reference guides to streamline your analysis and data processing tasks using commonly used bioinformatics commands.

What is Navi?

Navi is an interactive cheatsheet tool for the command line that helps users quickly find and execute commands without memorizing complex syntax. It allows users to browse and run pre-written or custom command-line snippets, dynamically displaying suggested values for arguments.

Why Use Navi?

• Saves Time – No need to memorize CLI commands.
• Reduces Errors – Eliminates copy-pasting from intermediate commands.
• Boosts Efficiency – Minimizes typing and speeds up workflow.
• Enhances Learning – Helps users discover new and useful one-liners.

Cheatsheets are written in a simple format and can be shared or customized to suit individual needs. Learn more in the official documentation. 🚀

This project intends to create a centralized resource of Navi cheatsheets related to computational biology, bioinformatics, and the dry lab side of biomedical research.

📂 Contents

The repository is organized by tool or language. The current tools include:

• BLAST/ - Cheatsheet for BLAST commands and usage.
• Perl/ - Cheatsheet for Perl, including common one-liners and scripts.
• AWK/ - Cheatsheet for AWK, with examples tailored for bioinformatics data manipulation.

This is a very, very short subset from the universe of bioinformatics tools and is intended to grow over time.

Have a tool you want added? Either open an issue stating the tool and what commands you want, or contribute it through a pull request.

📝 Cheatsheet Format

Each cheatsheet follows the Navi cheatsheet syntax. In these .cheat files you'll find:

• Command Descriptions: Lines starting with # explain the purpose of the commands.
• Executable Commands: Actual command lines with variable placeholders (e.g., <input_file>).
• Variable Suggestions: Lines starting with $ provide suggestions to autocomplete variable values.
• Tags: Lines starting with % denote the section tags, making it easy to filter and navigate within Navi.

For more details on the syntax and customization, please refer to the Navi documentation.

🚀 Getting Started

1. Install Navi:

   If you haven't installed Navi yet, follow the instructions on the Navi GitHub page.

   Highest yield options:

   • Using Homebrew: brew install navi

     or

   • Run install script: bash <(curl -sL https://raw.githubusercontent.com/denisidoro/navi/master/scripts/install)

     or

   • Build from source:

     git clone https://github.com/denisidoro/navi ~/.navi
     cd ~/.navi
     make install
     

2. Clone BioCheats:

   git clone https://github.com/grenkoca/biocheats.git
   cd biocheats

3. Load the Cheatsheets:

   navi --cheatsheets ./biocheats

🔍 Usage Examples

• BLAST Cheatsheet - Quickly reference commands for sequence similarity searches.
• Perl Cheatsheet - Discover Perl one-liners and script snippets for text processing.
• AWK Cheatsheet - Utilize AWK commands to filter, extract, and summarize data from various bioinformatics files.

🤝 Contributing

We welcome contributions to make BioCheats even more useful for the bioinformatics community! Here’s how you can help:

1️⃣ Fork the Repository

Click the Fork button on the top right corner of the GitHub page to create your own copy of the repository.

2️⃣ Create a New Branch

Develop your changes in a dedicated branch:

git checkout -b feature/your-feature-name

3️⃣ Make Your Changes

• Add or update cheatsheets following the Navi cheatsheet syntax.
• Update documentation if necessary.
• Ensure your cheatsheet commands are tested and working correctly.

4️⃣ Commit Your Changes

Commit your improvements with clear and descriptive commit messages:

git add .
git commit -m "Add/update cheatsheet for <tool/language>"

5️⃣ Push to Your Fork and Open a Pull Request

Push your branch to your fork and then open a pull request against the main branch:

git push origin feature/your-feature-name

Describe your changes and reference any related issues.

6️⃣ Code Review and Merge

Your pull request will be reviewed, and if everything looks good, it will be merged into the main branch.

🐛 Reporting Issues

If you encounter any issues or have suggestions for improvement, please open an issue on GitHub. We appreciate your feedback!

📜 License

This project is licensed under the MIT License. See the LICENSE file for details.

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Happy analyzing! 🎉