READemption 2.0.0

A RNA-Seq Analysis Pipeline

About

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) originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and from all domains of life. The functions which are accessible via a command-line interface cover read processing and aligning, coverage calculation, gene expression quantification, differential gene expression analysis as well as 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.

Documentation

Documentation can be found on here.

Installation

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

$ pip install READemption

Long version including a description of the requirements and how do you get them.

License

ICSL (Internet Systems Consortium license ~ simplified BSD license) - see LICENSE.txt

Development

• If possible follow the principal of “convention over configuration”. This means input file are copied/linked into a fixed location and the resulting files are placed in fixed locations.

• 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