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.. _docs_gp_relnote_3_0_0:

.. spelling:word-list::

    deduplication
    genpipes
    

GenPipes 3.0.0 Release Notes
============================a

A new release of the GenAP pipelines, now called GenPipes, 3.0.0 is now available.

What's new?
-----------

* New MethylSeq pipeline : DNA methylation detection for bisulfite whole genome or targeted sequencing analysis - applies routine sequencing methods on bisulfite-treated DNA to determine methylation status at CpG dinucleotides.
* New HicSeq pipeline : to analyze both Hi-C experimental and capture Hi-C data (Hi-C experiments allow researchers to understand chromosomal folding and structure using proximity ligation techniques)
* New RNA-Seq Light pipeline : quick and accurate transcript-level expression quantification and exploratory analysis
* Now each pipeline execution creates a JSON analysis file per analyzed sample in order to be able to monitor each sample analysis
* Added a new pipeline specific argument : protocol - this allows to execute a specific set of steps for a pipeline depending on the chosen protocol ; initially developed for HiC-Seq pipeline, will be progressively deployed to all the other pipelines
* Bug fixes
* Some modules were added/updated
* A new genome was installed :
    - Apis_mellifera.Amel_4.5

Quick! Where can I find it? I can't wait!
-----------------------------------------

* This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/GenAP_Pipes-3.0.0.tar.gz 

* The module mugqic/genpipes/3.1.3 is installed on Abacus, Guillimin, Mammouth-Mp2, Mammouth-Mp2b, Graham and Cedar clusters.

* The source code is in bitbucket: https://bitbucket.org/mugqic/genpipes