CellCoal

CellCoal simulates the somatic evolution of single cells using coalescent theory to generate genealogies and produce realistic single-cell diploid genotypes and single-nucleotide variants (SNVs).

Key Features:

• Coalescent Simulation: Constructs coalescent genealogies for somatic cell samples without recombination and can incorporate an outgroup cell.
• Mutation Introduction: Introduces mutations along simulated genealogies to generate single-nucleotide variants (SNVs).
• Single-Cell Genotype Production: Simulates diploid genotypes at single-cell resolution.
• Flexible Mutation Models: Supports multiple mutation models to represent diverse evolutionary scenarios.
• Sequencing Data Simulation: Models technical biases of single-cell sequencing including allelic imbalance, allelic dropout, amplification, and sequencing errors.
• Benchmarking Capability: Enables benchmarking of single-cell sequencing analysis methods by simulating diverse demographic histories and mutation scenarios.

Scientific Applications:

• Somatic evolution studies: Modeling lineage relationships and evolutionary dynamics in multicellular organisms and microbial communities.
• Mutation propagation and disease research: Investigating emergence and propagation of genetic variation and disease mechanisms such as cancer development.
• Method benchmarking: Validating and comparing bioinformatics tools for single-cell sequencing under realistic mutation and sequencing error models.

Methodology:

Generates coalescent genealogies for somatic cell populations (optionally with an outgroup) across diverse demographic histories, introduces mutations along those genealogies to produce SNVs, simulates diploid single-cell genotypes under various mutation models, and models sequencing biases including allelic imbalance, allelic dropout, amplification, and sequencing errors.