Centromeres are chromosomal regions historically understudied with sequencing technologies due to their repetitive nature and short-read mapping limitations. Recently, long-read sequencing data allowed their assembly and analysis at base-pair resolution, therefore novel methods employing this new type of resources are required to study their genetic and epigenetic features.
Results
We developed Centromere Dip Region (CDR)-Finder, an open-source tool to identify regions of hypomethylation within the centromeres of high-quality, contiguous genome assemblies. These regions are typically associated with a unique type of chromatin containing the histone H3 variant CENP-A, which marks the location of the kinetochore. CDR-Finder identifies the CDRs in large and short centromeres and outputs their coordinates as well as a plot for visualization, validation, and downstream analysis.
