==============
NGS Pipelines
==============

Genomics Pipelines
===================

.. toctree::
   :maxdepth: 1	

   pipelines/pipeline_annotations.rst   
   pipelines/pipeline_ancestral_repeats.rst
   pipelines/pipeline_chains.rst
   pipelines/pipeline_liftover.rst
   pipelines/pipeline_promotors.rst
   pipelines/pipeline_transfacmatch.rst

NGS Pipelines
==============

.. toctree::
   :maxdepth: 1	

   pipelines/pipeline_readqc.rst
   pipelines/pipeline_mapping.rst
   pipelines/pipeline_rnaseqtranscripts.rst
   pipelines/pipeline_rnaseqdiffexpression.rst
   pipelines/pipeline_transcriptome.rst
   pipelines/pipeline_peakcalling.rst
   pipelines/pipeline_rnaseqlncrna.rst   
   pipelines/pipeline_capseq.rst
   pipelines/pipeline_exome.rst
   pipelines/pipeline_expression.rst
   pipelines/pipeline_fusion.rst
   pipelines/pipeline_intervals.rst
   pipelines/pipeline_mapping_benchmark.rst
   pipelines/pipeline_medip.rst
   pipelines/pipeline_polyphen.rst
   pipelines/pipeline_variant_annotation.rst
   pipelines/pipeline_variants.rst

Other pipelines
=================

.. toctree::
   :maxdepth: 1	

   pipelines/pipeline_testing.rst
   pipelines/pipeline_quickstart.rst
   pipelines/pipeline_template.rst
   pipelines/pipeline_benchmark_rnaseqmappers.rst
   pipelines/pipeline_cufflinks_optimization.rst
   pipelines/pipeline_mappability.rst

Obsolete pipelines
====================

.. toctree::
   :maxdepth: 1	

   pipelines/pipeline_fastqToBigWig.rst
   pipelines/pipeline_chipseq.rst
   pipelines/pipeline_rnaseq.rst