dupRadar

dupRadar is a tool for quality control assessment of RNA-Seq data sets that help to distinguish natural duplication due to high expression from duplication induced by artifacts. This tool assesses the fraction of duplicate reads per gene dependent on expression level. It is particularly useful for low-input and single-cell RNA-Seq data sets, where quality control is a crucial step in NGS data analysis.

In RNA-Seq data sets, it is not easy to differentiate between artifactual reads and normal read duplication due to the natural over-sequencing of highly expressed genes. This is especially true when working with little input material or single cells. dupRadar addresses this challenge by providing a means to distinguish the fraction of reads originating from natural duplication due to high expression from the fraction induced by artifacts.

Apart from the Bioconductor package, dupRadar also provides shell scripts that enable easy integration into processing pipelines. This feature makes it a go-to tool for researchers with NGS data sets. The tool is designed to easily integrate as a default quality control metric into standard analysis pipelines.