READemption - A RNA-Seq Analysis Pipeline

READemption in a nutshell

READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 (Pubmed)) originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and from all domains of life. The functions which are accessible via a command-line interface cover read processing and aligning, coverage calculation, gene expression quantification, differential gene expression analysis as well as visualization. In order to set up and perform analyses quickly READemption follows the principal of convention over configuration: Once the input files are copied/linked into defined folders no further parameters have to be given. Still, READemption’s behavior can be adapted to specific needs of the user by parameters.


READemption can be download from its PyPI page. Please read the installation instructions.

Source code

The source code of READemption can be found at


If you apply READemption in your data analysis please cite the following publication: READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data. Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma. 2014, Bioinformatics, Aug 13. Fulltext, Pre-print at bioRxiv.


For question and requests feel free to contact Konrad Förstner <>