Graph Peak Caller

Graph Peak Caller identifies transcription factor binding sites (peaks) from ChIP-seq data aligned to graph-based reference genomes.

Key Features:

• Graph-Based Genome Compatibility: Operates on graph-based reference genomes to represent individual genetic variation beyond linear references.
• Generalization of MACS2: Extends MACS2 peak-calling functionality to work within a graph-based framework.
• Variant Detection Within Peaks: Uses pan-genome reference graphs to identify genetic variants located within transcription factor peaks that may be absent from linear references.
• Motif Enrichment Analysis: Detects peaks that exhibit higher motif enrichment compared to peaks called by MACS2.

Scientific Applications:

• Personalized Medicine: Identifies variant-specific peaks to study how genetic differences influence disease susceptibility and treatment response.
• Functional Genomics: Enables exploration of regulatory elements that vary between individuals to inform gene regulation studies.
• Comparative Genomics: Supports analyses with pan-genomes for comparative studies across strains or species to discover conserved and divergent regulatory features.

Methodology:

Aligns ChIP-seq data to graph-based reference genomes, builds pan-genome graphs using the vg toolkit, and applies a generalization of MACS2 for peak calling on graph-based references.