# Gtars

High-performance toolkit for genomic interval analysis in Rust with Python bindings.

- Repository: https://github.com/LeonChaoX/qinyan-academic-skills (996 stars)
- Category: Data and ML
- License: Unknown
- Last updated: 2026-07-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add LeonChaoX/qinyan-academic-skills --skill gtars -g -a claude-code -y`
Codex: `npx skills add LeonChaoX/qinyan-academic-skills --skill gtars -g -a codex -y`
Cursor: `npx skills add LeonChaoX/qinyan-academic-skills --skill gtars -g -a cursor -y`
Gemini CLI: `npx skills add LeonChaoX/qinyan-academic-skills --skill gtars -g -a gemini-cli -y`

## Description

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Gtars: Genomic Tools and Algorithms in Rust

## Overview

Gtars is a high-performance Rust toolkit for manipulating, analyzing, and processing genomic interval data. It provides specialized tools for overlap detection, coverage analysis, tokenization for machine learning, and reference sequence management.

Use this skill when working with:
- Genomic interval files (BED format)
- Overlap detection between genomic regions
- Coverage track generation (WIG, BigWig)
- Genomic ML preprocessing and tokenization
- Fragment analysis in single-cell genomics
- Reference sequence retrieval and validation

## Installation

### Python Installation

Install gtars Python bindings:

```bash
uv uv pip install gtars
```

### CLI Installation

Install command-line tools (requires Rust/Cargo):

```bash
# Install with all features
cargo install gtars-cli --features "uniwig overlaprs igd bbcache scoring fragsplit"

# Or install specific features only
cargo install gtars-cli --features "uniwig overlaprs"
```

### Rust Library

Add to Cargo.toml for Rust projects:

```toml
[dependencies]
gtars = { version = "0.1", features = ["tokenizers", "overlaprs"] }
```

## Core Capabilities

Gtars is organized into specialized modules, each focused on specific genomic analysis tasks:

### 1. Overlap Detection and IGD Indexing

Efficiently detect overlaps between genomic intervals using the Integrated Genome Database (IGD) data structure.

**When to use:**
- Finding overlapping regulatory elements
- Variant annotation
- Comparing ChIP-seq peaks
- Identifying shared genomic features

**Quick example:**
```python
import gtars

# Build IGD index and query overlaps
igd = gtars.igd.build_index("regions.bed")
overlaps = igd.query("chr1", 1000, 2000)
```

See `references/overlap.md` for comprehensive overlap detection documentation.

### 2. Coverage Track Generation

Generate coverage tracks from sequencing data with the uniwig module.

The rest: https://github.com/LeonChaoX/qinyan-academic-skills/blob/HEAD/skills/05-生物信息与基因组学/gtars/SKILL.md