READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and from all domains of life.
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READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data.
Förstner KU, Vogel J, Sharma CM.
Bioinformatics. 2014 Aug 13. pii: btu533.