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