SomaticSiMu

SomaticSiMu simulates single and double base pair substitutions and single base pair insertions and deletions by imposing predefined mutational signatures on input genomic sequences to generate simulated DNA sequences and mutational catalogues for mutational signature analysis.

Key Features:

• Simulated mutation types: Generates single base substitutions, double base substitutions, and single base insertions and deletions within genomic sequences.
• Imposition of mutational signatures: Applies predefined mutational signatures to an input genomic sequence to create controlled mutational patterns.
• Controlled mutation rates: Allows specification of mutation rates to vary mutation burden across simulated datasets.
• Outputs: Produces modified DNA sequences and comprehensive mutational catalogues for downstream analysis.

Scientific Applications:

• Validation of classification tools: Provides simulated datasets with known mutation types and burdens to assess DNA sequence classification algorithm accuracy and sensitivity.
• Benchmarking mutational signature extraction: Enables evaluation of mutational signature extraction methodologies using catalogues with imposed signatures.
• Supervised machine learning testing: Supplies ground-truth labelled mutation datasets for training and testing supervised machine learning classifiers.

Methodology:

SomaticSiMu takes an input genomic sequence and applies predefined mutational signatures to simulate single and double base substitutions and single base insertions and deletions, then outputs the modified DNA sequences and corresponding mutational catalogues.