gtars-scatrs

SCATRS (Single-Cell ATAC-seq Region Simulator) - High-performance single-cell ATAC-seq fragment simulation.

Features

• Realistic fragment generation based on empirical distributions
• Cell type-specific simulation
• Quality score modeling
• Batch and barcode generation
• Parallel processing with rayon

Usage

Command Line

scatrs simulate \
  --peaks peaks.bed \
  --cells 10000 \
  --output fragments.tsv.gz

From Rust

use gtars_scatrs::{Simulator, SimulationParams};

let params = SimulationParams {
    num_cells: 10000,
    mean_fragments_per_cell: 5000,
    ..Default::default()
};

let simulator = Simulator::new(params);
simulator.run("peaks.bed", "output.tsv.gz")?;

Simulation Parameters

• Number of cells
• Fragment size distribution
• Coverage depth
• Cell type proportions
• Technical noise parameters

Output Format

Standard 10x Genomics fragment file format:

chr1    1000    1500    AAACCCAAGAAACACT-1    1
chr1    2000    2300    AAACCCAAGAAACACT-1    1