clIGV - command line Interactive Genome Viewer

A fast, interactive genome browser for the command line. clIGV (command line Interactive Genome Viewer) allows you to view genomic sequences, alignments, and variants directly in your terminal with a simple interface.

Features

• View reference genome sequences from FASTA files
• Display variant calls from VCF files
• Visualize read alignments from BAM files with coverage tracks
• Intuitive keyboard navigation and zooming
• Color-coded display with both dark and light theme options
• Tag-based read coloring for highlighting specific attributes
• Scales well for both small regions and larger genomic intervals

Installation

Using pip

pip install cligv

Using conda

conda install -c conda-forge cligv

From source

git clone https://github.com/jonasfreudig/cligv.git
cd cligv
pip install -e .

Quick Start

# Basic usage with just a reference genome
cligv reference.fasta

# View with variants
cligv reference.fasta -v variants.vcf.gz

# View with read alignments
cligv reference.fasta -b alignments.bam

# Load directly to a specific region
cligv reference.fasta -r chr1:1000-2000

# Full example with all options
cligv reference.fasta -v variants.vcf.gz -b alignments.bam -r chr1:1000-2000 -t ha --light-mode

Navigation

• a - Move left
• d - Move right
• w - Zoom in
• s - Zoom out
• g - Go to a specific region
• t - Toggle between dark and light mode
• q - Quit

Requirements

• Python 3.8+
• pysam
• rich

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add some amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

License

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

Acknowledgments

• Inspired by tools like IGV, samtools tview, ASCIIGenome, and other genomic viewers
• Thanks to all contributors and users for their feedback and suggestions