NUCLIZE is a toolkit for defining histone variants and modification at the resolution of single nucleosome by synergistic analysis of histone variants and modification data from ChIP-Seq and nucleosome mapping data from native MNase-Seq. This toolkit includes three major modules for nucleosome peak calling, nucleosome-based histone variants and modification peak calling, and comparison of NUCLIZE-analyzed histone variants and modification data between samples. Thus, each NUCLIZE-analyzed histone variant or modification is tied to its original nucleosome. Meanwhile, NUCLIZE can also analyze histone variants and modification peaks and nucleosome peaks called by other programs.