Juicer

Juicer processes large-scale Hi-C sequencing data to generate normalized, high-resolution contact maps for analysis of three-dimensional genome architecture.

Key Features:

• Data handling: Processes terabase-scale Hi-C data derived from experiments that map physical interactions between genomic regions.
• Raw data processing and normalization: Converts raw sequencing data into normalized contact maps.
• Multi-resolution matrices: Generates compressed contact matrices at multiple resolutions to enable analysis across genomic scales.
• Automated structural annotation: Annotates structural features such as topologically associating domains (TADs), loops, and other significant genomic elements within contact maps.
• Contact map generation: Produces high-resolution contact maps from processed Hi-C reads for downstream analysis of 3D genome structure.

Scientific Applications:

• 3D genome architecture analysis: Enables study of the spatial arrangement of the genome using contact maps.
• Gene regulation studies: Facilitates investigation of regulatory interactions such as enhancer–promoter contacts via contact frequency patterns.
• Chromosomal interaction and disease research: Supports analysis of chromosomal interactions and the structural basis of genetic diseases.
• High-throughput Hi-C projects: Suited for producing detailed 3D genomic maps in large-scale, high-throughput sequencing settings.

Methodology:

Processes terabase-scale Hi-C reads, converts raw sequencing data into normalized contact maps, generates compressed contact matrices at multiple resolutions, and automatically annotates TADs, loops, and other genomic elements within the maps.