title: READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data.
abstract: RNA-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.
  
  
  METHODS
  READemption 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).
authors.affiliation: 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.
authors.forename: Konrad U
authors.initials: KU
authors.lastname: Förstner
authors.affiliation: Institute for Molecular Infection Biology and Research Centre for Infectious Diseases (ZINF), University of Würzburg, D-97080 Würzburg, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
authors.affiliation: Institute for Molecular Infection Biology and Research Centre for Infectious Diseases (ZINF), University of Würzburg, D-97080 Würzburg, Germany.
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software