Metadata-Version: 2.0
Name: mgkit
Version: 0.2.2
Summary: Metagenomics Framework
Home-page: https://bitbucket.org/setsuna80/mgkit/
Author: Francesco Rubino
Author-email: rubino.francesco@gmail.com
License: GPL2+
Keywords: metagenomics library biology bioinformatics snps gff fasta
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: numpy (>=1.9.2)
Requires-Dist: pysam (>=0.8.2.1)
Requires-Dist: pandas (>=0.16.2)
Requires-Dist: scipy (>=0.15.1)
Requires-Dist: semidbm (>=0.5.1)
Requires-Dist: enum34
Provides-Extra: R
Requires-Dist: rpy2 (>=2.3.8); extra == 'R'
Provides-Extra: htseq
Requires-Dist: HTSeq (>=0.6.0); extra == 'htseq'
Provides-Extra: semidbm
Requires-Dist: semidbm (>=0.5.1); extra == 'semidbm'

MGKit: Metagenomics Framework
=============================

The aim of this library [#]_ is to provide a series of useful modules and packages to make it easier to build custom pipelines for metagenomics or any kind of bioinformatics analysis. It integrates other well known python libraries in bioinformatics, like `HTSeq <http://www-huber.embl.de/users/anders/HTSeq/>`_, `pysam <https://code.google.com/p/pysam/>`_, `numpy <http://www.numpy.org>`_ and `scipy <http://www.scipy.org>`_.

A tutorial pipeline is provided in the `Documentation <http://pythonhosted.org//mgkit/pipeline/tutorial.html>`_. Data and scripts used in the documentations are available at [#]_.

A discussion mailing list is available at `mgkit-users <https://groups.google.com/forum/#!forum/mgkit-users>`_.

Citing
------

Rubino, F. and Creevey, C.J. 2014. MGkit: Metagenomic Framework For The Study Of Microbial Communities. . Available at: `figshare <http://figshare.com/articles/MGkit_Metagenomic_Framework_For_The_Study_Of_Microbial_Communities/1269288>`_ [doi:10.6084/m9.figshare.1269288].`

a citation is also available using the *mgkit.cite()* function or using the `--cite` option on all scripts included. This will ouput the following

Links
-----

.. [#] `<https://bitbucket.org/setsuna80/mgkit>`_
.. [#] `<http://dx.doi.org/10.6084/m9.figshare.1588384>`_


