fluff: exploratory analysis and visualization of high-throughput sequencing data
Abstract
Summary
In this application note 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, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://fluff.readthedocs.org">http://fluff.readthedocs.org.</ext-link>
Availability
fluff is implemented in Python and runs on Linux. The source code is freely available for download at <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://github.com/simonvh/fluff">http://github.com/simonvh/fluff.</ext-link>
Contact
<email>s.vanheeringen@science.ru.nl</email>
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