Genomic Tools and Analysis in Rust (Gtars)

About

Gtars is a high-performance toolkit designed for researchers and developers working with large-scale genomic data. It bridges the gap between Rust's performance and Python's flexibility, offering specialized modules for IGD-based overlap detection, fragment processing, and coverage track generation. Whether you are building deep learning models for genomics requiring efficient tokenization or performing standard bioinformatic operations like BED file manipulation and reference sequence validation, Gtars provides the optimized infrastructure needed for computational genomics.

Key Features

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• Efficient coverage track generation (WIG/BigWig) from sequencing data with uniwig
• Comprehensive reference sequence management and GA4GH refget protocol support
• Ultra-fast genomic interval overlap detection using Integrated Genome Database (IGD) indexing
• Advanced genomic tokenization for preprocessing deep learning and ML models
• Parallelized fragment processing for single-cell genomics and ATAC-seq data

Use Cases

• Generating high-resolution accessibility profiles and coverage tracks for genome browsers
• Identifying overlapping regulatory elements and variant annotations across large BED datasets
• Preprocessing genomic sequences into discrete tokens for training transformer models