A collection of perl scripts for NGS analysis, written by Adam Burholder, Sara Grimm and David Fargo of the National Institute of Environmental Health Sciences (NIEHS). These scripts have been used in a number of collaborative studies betwen the Adelman lab and the NIEHS Center for Integrative Bioinformatics.
Examples: Nechaev et al. Science 2010, Gilchrist et al. Genes Dev 2012, Core et al. Cell Reports 2012, Henriques et al. Mol Cell 2013, Scruggs et al. Mol Cell 2015, Williams et al. Mol Cell 2015, Henriques et al. Genes Dev 2018.
These modular perl scripts allow a user to perform common tasks involved in visualization and analysis of NGS data. They are provided here for general use.
The names of each file are fairly self-explanatory about the basic tasks each script is intended for, and readme files provided give detailed usage information.