READemption 0.2.2

A RNA-Seq Analysis Pipeline

About

READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed at the IMIB/ZINF to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010) originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and originating from all domains of life and is under active development. The subcommands which are accessible viaq command-line interface cover read processing and aligning, coverage plot generation, gene expression quantification as well as differential gene expression analysis. READemption was applied to analyze numerous data sets. In order to set up analyses quickly READemption follows the principal of “convention over configuration”: Once the input files are copied into defined folders no further parameters have to be given. Still, READemption’s behavior can be adapted to specific needs of the user.

Documentation

Documentation can be found on here.

Installation

Short version (if you have all the requirements installed):

$ pip install READemption

Long version (what are the requirements and how do you get them)

License

ICSL - see LICENSE.txt

Development

• If possible follow the principal of “convention over configuration”. This means input file are into a fixed location and the result file are placed in fixed location.

• The classes should be path agnostic as far a possible. The controller is taking care of that and calls them adequately.

• The git braching model is very close to the one proposed here. There two main branches:

  • master

  • dev(elopment)

  And there are further supporting branches:

  • feature branches - branched off and back to the dev branch

  • release branches - branched off from dev and merged back into dev and master

  • hotfix branches - branched off from master and merged back into dev and master