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 bioconda 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

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.

Fork the repository
Create your feature branch (git checkout -b feature/amazing-feature)
Commit your changes (git commit -m 'Add some amazing feature')
Push to the branch (git push origin feature/amazing-feature)
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