HiCapTools

HiCapTools performs targeted probe design and contact analysis for chromosome conformation capture methods (T2C, chi-C, and HiCap) to detect and statistically evaluate physical contacts between genomic regions for studies of 3D genome architecture and gene regulation.

Key Features:

• Probe Design: Designs two sequence capture probes per genomic feature while avoiding repeat elements and non-unique regions to specifically capture targeted restriction fragments.
• Data Analysis Suite: Processes sequencing alignment files to detect and report genomic proximities at the restriction fragment level and performs isoform-aware analysis for gene features.
• Statistical Evaluation: Assesses the significance of detected contact frequencies using an empirically derived background distribution.

Scientific Applications:

• Genome architecture and gene regulation: Identifies physical contacts between regulatory elements and genes to study how 3D folding influences gene regulation and chromatin dynamics.
• Chromatin dynamics and cellular function: Maps targeted physical interactions to investigate relationships between spatial genome organization and cellular processes.
• GWAS variant-to-gene mapping: Supports linking disease-associated variants from GWAS to candidate target genes via detected physical contacts.

Methodology:

Computationally designs two capture probes per feature avoiding repeats and non-unique regions, processes sequencing alignment files to map contacts at the restriction fragment level with isoform-aware handling of gene features, and evaluates contact significance using an empirically derived background distribution.