• Konrad U Förstner, Jörg Vogel, and Cynthia M Sharma.
• Institute for Molecular Infection Biology and Research Centre for Infectious Diseases (ZINF), University of Würzburg, D-97080 Würzburg, Germany Institute for Molecular Infection Biology and Research Centre for Infectious Diseases (ZINF), University of Würzburg, D-97080 Würzburg, Germany.
• Bioinformatics. 2014 Dec 1; 30 (23): 3421-3.

UnlabelledRNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. To draw biological conclusions based on RNA-Seq data, several steps, some of which are computationally intensive, have to be taken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes and RNA immunoprecipitated with proteins, not only from bacteria but also from eukaryotes and archaea.Availability And ImplementationREADemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http://pythonhosted.org/READemption (DOI:10.6084/m9.figshare.977849).© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

11 keywords...

hide…