SCSIM

SCSIM simulates correlated single-cell and bulk next-generation DNA sequencing data within a hierarchical sampling framework to generate realistic datasets for evaluating genomic analysis methods.

Key Features:

• Hierarchical sampling: Simulates DNA sequencing data from nested group structures that include both single-cell and bulk tissue samples to model biological correlations.
• Next-generation sequencing output: Generates NGS DNA sequencing data reflecting single-cell and bulk sample characteristics.
• Configuration file-driven setup: Uses a simple configuration file to define experimental designs and sampling hierarchies.
• Pipeline integration: Produces data compatible with downstream analysis pipelines for direct use in variant callers and other genomic tools.

Scientific Applications:

• Assessment of variant callers: Evaluates performance of variant calling algorithms using realistic correlated single-cell and bulk datasets.
• Development of analytical methods: Provides controlled simulated data for creating and testing novel genomic analysis approaches.
• Benchmarking and validation: Enables rigorous benchmarking of genomic tools across diverse hierarchical sampling contexts.

Methodology:

Simulates DNA sequencing reads for nested hierarchical groups comprising single-cell and bulk samples to capture inherent correlations between biological units.