Fluff: Exploratory analysis and visualization of high-throughput sequencing data

Abstract

Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluffincludes a tool to generate genomic profiles. As command-line tools, the fluffprograms can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluffis implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff.