NucTools: software package for the analysis of chromatin feature occupancy profiles from high-throughput sequencing data
External link: https://homeveg.github.io/nuctools
Developed by Yevhen Vainshtein and Vladimir Teif
NucTools is a suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between different experimental conditions, and the estimation of the changes of integral chromatin properties such as the nucleosome repeat length. Furthermore, NucTools facilitates the annotation of nucleosome occupancy with other chromatin features like binding of transcription factors or architectural proteins, and epigenetic marks like histone modifications or DNA methylation.
Vainshtein Y., Rippe K. and Teif V.B. (2017). NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics 18, 158. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3580-2