Motivation: Tag density plots are very important to intuitively reveal biological phenomena from capture-based sequencing data by visualizing the normalized read depth in a region.

Results: We have developed iTagPlot to compute tag density across functional features in parallel using multicores and a grid engine and to interactively explore it in a graphical user interface. It allows us to stratify features by defining groups based on biological function and measurement, summary statistics and unsupervised clustering.

Availability and implementation: http://sourceforge.net/projects/itagplot/.

Contact: jechoi@gru.edu and jeochoi@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.