Apr 3, 2014

READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data

BioRxiv : the Preprint Server for Biology
Konrad U FörstnerCynthia M Sharma


Summary RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. In order 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, RNA immunoprecipitated with proteins, not only from bacteria, but also from eukaryotes and archaea. Availability and Implementation 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). Contact cynthia.sharma{at}uni-wuerzburg.de; konrad.foerstner{at}uni-wuerzburg.de

  • References
  • Citations


  • We're still populating references for this paper, please check back later.
  • References
  • Citations


  • This paper may not have been cited yet.

Mentioned in this Paper

Deep Sequencing

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.


Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.