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gtars

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A high-performance Rust toolkit (with Python bindings and a CLI) for genomic interval analysis; use it when you need fast overlap queries, coverage track generation, genomic tokenization for ML, reference sequence verification, or fragment processing.

scientific-skills/Data Analysis/gtars/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- **Overlap and set operations on genomic intervals** (e.g., peak/promoter overlap, variant annotation, shared-feature detection).
- **Coverage track generation** from interval-like inputs (e.g., ATAC-seq/ChIP-seq/RNA-seq coverage for visualization in genome browsers).
- **Machine-learning preprocessing** where genomic regions must be converted into discrete **tokens** (e.g., Transformer-style models, geniml-style pipelines).
- **Reference sequence management and verification** (e.g., subsequence retrieval, digest calculation aligned with GA4GH refget concepts).
- **Single-cell fragment workflows** (e.g., splitting fragments by barcode/cluster, scoring fragments against reference region sets).

## Key Features

- **Rust performance** with low overhead; designed for large genomic datasets.
- **Python bindings** for integration into analysis notebooks/pipelines.
- **CLI tooling** for batch processing and shell workflows.
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