Gtars Genomic Analysis Toolkit

About

Gtars is a high-performance toolkit designed for computational biology and genomic machine learning workflows, offering high-speed processing of genomic intervals, BED files, and coverage tracks. It leverages Rust's performance to provide efficient overlap detection via IGD indexing, reference sequence management via GA4GH refget, and specialized tokenization for training deep learning models on genomic data. This skill is essential for bioinformaticians and researchers needing to handle large-scale genomic datasets with minimal memory overhead and maximum execution speed through both CLI and Python interfaces.

Key Features

• Fragment processing for single-cell ATAC-seq analysis
• Genomic sequence tokenization for machine learning models
• Coverage track generation for WIG and BigWig formats
• 81 GitHub stars
• Reference genome management with GA4GH refget support
• High-performance overlap detection using IGD indexing

Use Cases

• Identifying overlaps between ChIP-seq peaks and regulatory elements
• Generating coverage tracks for sequencing data visualization
• Preprocessing genomic regions for transformer-based ML models