snHiC

snHiC implements a Snakemake pipeline to process Hi-C Paired-End fastq files into multi-resolution contact matrices and to perform quality control, normalization, detection of topologically associating domains (TADs), chromatin loops and stripes, differential contacts and compartment analyses, and grouped analyses to study three-dimensional genome organization.

Key Features:

• End-to-End Workflow: Handles all stages of Hi-C data processing from Paired-End fastq files to downstream analyses.
• Data Quality Control and Normalization: Includes modules for quality control checks and normalization of Hi-C datasets.
• Resolution Flexibility: Generates contact matrices at multiple resolutions within a single run.
• Grouped Analyses: Supports aggregation of individual samples into user-defined groups for comparative analyses.
• Structural Feature Detection: Detects topologically associating domains (TADs), chromatin loops, and stripes.
• Differential Analysis Capabilities: Performs differential contacts and compartment analyses.
• Snakemake-based Workflow and Environment: Implements workflows with Snakemake and provides a conda environment file (snHiC/workflow/envs/snHiC_conda_env_stable.yaml) for consistent computational environments.

Scientific Applications:

• Gene Regulation: Enables analysis of chromatin interactions relevant to transcriptional regulation and enhancer–promoter contacts.
• Chromosomal Architecture: Facilitates investigation of genome folding, TAD organization, loops, and stripe structures.
• Disease Mechanisms: Supports identification of altered chromatin interactions and compartments associated with disease states.
• Comparative Genomics: Allows comparative and grouped analyses across samples or conditions to detect differential interactions.
• Epigenetic Studies: Assists studies linking 3D genome organization to epigenetic states and modifications.

Methodology:

Orchestrates the workflow using Snakemake and supplies a conda environment file at snHiC/workflow/envs/snHiC_conda_env_stable.yaml.