:orphan:

.. _docs_gp_relnote_3_3_0:

.. spelling:word-list::

     genpipes

GenPipes 3.3.0 Release Notes
============================

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

* Two new steps were added in the `HiC Sequencing Pipeline <https://genpipes.readthedocs.io/en/genpipes-v4.6.0/user_guide/pipelines/gp_hicseq.html>`_:

  - *Reproducibility Scores*: R package `hicrep <https://bioconductor.org/packages/release/bioc/html/hicrep.html>`_ is used to calculate inter-chromosomal reproducibility scores.
  - *Quality Scores*: `QuASAR <https://www.biorxiv.org/node/62284.full>`_ (part of `hifive <https://github.com/bxlab/hifive>`_ suite), is used to calculate quality score per chromosome.

Quick! Where can I find it? I can't wait! 
------------------------------------------
 
* This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-3.3.0.tar.gz

* The module mugqic/genpipes/3.3.0 is installed on Abacus (MGC), Béluga, Graham and Cedar clusters.

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

* For more documentation, please refer to: https://genpipes.readthedocs.io/

Where is the detailed ChangeLog? 
================================= 
A ChangeLog (`CHANGELOG.md <https://bitbucket.org/mugqic/genpipes/src/master/CHANGELOG.md>`_) is available in the archive as well as in the repository.

Since we use git, there are many ways to get the details in many formats. 
One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert, 
which lists the commits by tag and author: 

https://raw.github.com/sebhtml/ray/master/scripts/dump-ChangeLog.sh 

Enjoy our pipelines on the many clusters where they are installed!

.. _vcftool imiss: http://vcftools.sourceforge.net/man_latest.html