Sim3C

Sim3C simulates sequence data from chromosome conformation capture (3C) and Hi-C protocols to model genome spatial organization in eukaryotic genomes and metagenomes for algorithm development and experimental design.

Key Features:

• Simulation of spatial structures: Models the fundamental spatial organization observed in Hi-C and 3C datasets, including the distance-decay relationship of proximity ligation events.
• Intra- and inter-chromosomal interactions: Differentiates and simulates interactions within single chromosomes and between different chromosomes.
• Cellular structure constraints: Incorporates structural constraints imposed by cellular environments into simulated contact patterns.
• Topologically Associating Domains (TADs): Models the 3D structure of randomly generated TADs to reflect domain-level genome architecture.
• Error modeling: Simulates common experimental errors such as spurious proximity ligation events and sequencing errors.
• Input-driven simulation: Generates simulated 3C/Hi-C sequencing data from user-provided input parameters and reference genome sequences.

Scientific Applications:

• Algorithm testing: Provides realistic simulated Hi-C/3C datasets for developing and validating computational methods that analyze chromatin interaction data.
• Experimental design: Enables evaluation of experimental parameters such as sequencing depth and enzyme choice using simulated datasets to inform study design.

Methodology:

Sim3C takes simple input parameters and reference genome sequences to generate simulated Hi-C and 3C sequencing data, modeling spatial genome structures (distance-decay, intra/inter-chromosomal interactions, cellular constraints, randomly generated TADs) and experimental errors (spurious proximity ligation events and sequencing errors).