Metadata-Version: 1.1
Name: mbin
Version: 1.1.0
Summary: mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
Home-page: https://github.com/fanglab/mbin
Author: John Beaulaurier
Author-email: john.beaulaurier@gmail.com
License: CC BY-NC-SA 4.0 license
Description: =============
        mBin overview
        =============
        
        
        .. image:: https://img.shields.io/pypi/v/mbin.svg
                :target: https://pypi.python.org/pypi/mbin
        
        .. image:: https://img.shields.io/travis/fanglab/mbin.svg
                :target: https://travis-ci.org/fanglab/mbin
        
        .. image:: https://readthedocs.org/projects/mbin/badge/?version=latest
                :target: https://mbin.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
        
        The mBin pipeline is designed to discover the unique signals of DNA methylation in metagenomic SMRT sequencing reads and leverage them for organism binning of assembled contigs or unassembled reads. Because *all* cellular DNA is modified by the same set of methyltransferases encoded in the genome, DNA methylation signals can be used for binning not just chromosomal sequences, but also extrachromosomal mobile genetic elements like plasmids.
        
        The pipeline consists of four routines:
        
        1. *buildcontrols*: Gets unmethylated IPD values for motifs from whole-genome amplified (WGA) sequencing 
        2. *filtermotifs*: Identifies methylated motifs in native metagenomic sequencing
        3. *methylprofiles*: Creates methylation profiles for sequences using specified motifs 
        4. *mapfeatures*: Visualizes landscape of methylation features across all sequences
        
        Documentation
        -------------
        For a comprehensive guide on how to install and run mBin, please see the full `documentation <https://mbin.readthedocs.io/en/latest/>`__.
        
        
        Citations
        ---------
        Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett E, Faith J, Sebra R, Schadt EE, Fang G. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. *Nature Biotechnology* (2017). doi:10.1038/nbt.4037.
        
        Credits
        ---------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        
        =======
        History
        =======
        
        1.0.0 (2017-06-13)
        ------------------
        
        * First release on PyPI.
        
Keywords: mbin methylation sequencing binning metagenomic
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: License :: Free for non-commercial use
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
