READemption - A RNA-Seq Analysis Pipeline

Table of content

• Installation and updating
• Docker image
• READemption’s subcommands
• Fragment building for paired-end reads
• Performing example analyses
• Troubleshooting
• License
• Versions/Change log

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 it has been extended to process data generated in different experimental setups e.g. Dual RNA-Seq (Westermann et al., Nature, 2016 (Pubmed)) and from all domains of life. READemption features handling of:

• single and multi-species projects

The functions which are accessible via a command-line interface cover:

• read processing
• aligning
• coverage calculation
• gene expression quantification
• differential gene expression analysis
• 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.

Download

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

Source code

The source code of READemption can be found at https://github.com/foerstner-lab/READemption.

Cite

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.

Contact

For question and requests feel free to contact Konrad Förstner <foerstner@zbmed.de>