CapSim

CapSim simulates targeted sequencing with capture probes to model genome fragmentation, probe hybridization dynamics, and sequencing on Illumina and PacBio platforms for evaluation of probe design and experimental parameters.

Key Features:

• Simulation of Fragmentation: Models fragmentation of a genome sequence to generate DNA fragments prior to hybridization.
• Probe Hybridization Dynamics: Simulates hybridization interactions between capture probes and target sequences to predict probe-target binding behavior.
• Sequencing Simulation on Multiple Platforms: Produces simulated sequencing of captured fragments for Illumina and PacBio platforms.

Scientific Applications:

• Probe Design Efficiency Evaluation: Uses hybridization simulation to assess the efficiency of probe designs before experiments.
• Performance Optimization: Enables evaluation of parameters across fragmentation, hybridization, and sequencing to optimize experimental conditions.
• Analysis Pipeline Performance Testing: Generates simulated data for testing and refinement of downstream analysis pipelines.

Methodology:

Requires a genome sequence and a set of probes as input; simulates genome fragmentation, hybridization dynamics between probes and target sequences, and sequencing of captured fragments.