CENdetectHOR: a comprehensive tool for CENtromere profiling and HOR detection

Centromeres are essential for accurate chromosome segregation and are characterized by long arrays of repetitive satellite DNA, showing extensive variation in sequence, length, and organization across species. Despite extensive research, fully characterizing centromeric DNA has been challenging due to its repetitive nature and rapid evolution. Here, we present CENdetectHOR, a computational tool to identify and analyze higher-order repeat (HOR) arrays in centromeric regions across diverse organisms, requiring no a priori information. We validate its efficacy using human and arabidopsis genomes, demonstrating its ability to reveal the complexity and diversity of centromeric architectures. CENdetectHOR also recognizes HOR variants, elucidating interindividual and interspecific variations in centromeric regions. These findings establish CENdetectHOR as a powerful, versatile, and rapid tool for advancing research on centromere structure, evolution, and function.