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A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.

Contents:

.. toctree::
   :maxdepth: 2

   contents/introduction
   contents/installation
   contents/pipelines
   contents/testing
   contents/configuration
   contents/parallel
   contents/cwl
   contents/cloud
   contents/outputs
   contents/code
   contents/internals
   contents/presentations
   contents/teaching
   contents/citations


Indices and tables