Metadata-Version: 1.0
Name: refinem
Version: 0.0.20
Summary: A toolbox for improving population genomes.
Home-page: http://pypi.python.org/pypi/refinem/
Author: Donovan Parks
Author-email: donovan.parks@gmail.com
License: GPL3
Description: RefineM
        =======
        
        **[This project is in active development and not currently recommended for public use.]**
        
        
        `version status <https://pypi.python.org/pypi/refinem>`_
        
        `downloads <https://pypi.python.org/pypi/refinem>`_
        
        RefineM is a set of tools for improving population genomes. It provides methods designed to improve the completeness of a genome along with methods for identifying and removing contamination. RefineM comprises only part of a full genome QC pipeline and should be used in conjunction with existing QC tools such as `CheckM <https://github.com/Ecogenomics/CheckM/wiki>`_. The functionality currently planned is:
        
        *Improve completeness:*
        
        * identify contigs with similarity to specific reference genome(s)
        
        * identify contigs with compatible GC, coverage, and tetranucleotide signatures
        
        * indetify partial population genomes which should be merged together (requires `CheckM <https://github.com/Ecogenomics/CheckM/wiki>`_)
        
        
        *Reducing contamination:*
        
        * taxonomically classify contigs within a genome in order to identify outliers
        
        * identify contigs with divergent GC content, coverage, or tetranucleotide signatures
        
        * identify contigs with a coding density suggestive of a Eukaryotic origin
        
        
        
        Install
        -------
        
        The simplest way to install this package is through pip:
        > sudo pip install refinem
        
        This package requires numpy to be installed and makes use of the follow bioinformatic packages:
        
        * `prodigal <http://prodigal.ornl.gov/>`_: Hyatt D, Locascio PF, Hauser LJ, Uberbacher EC. 2012. Gene and translation initiation site prediction in metagenomic sequences. *Bioinformatics* 28: 2223-2230.
        
        * `blast+ <http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>`_: Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. *BMC Bioinformatics* 10:421: doi: 10.1186/1471-2105-10-421.
        
        * `diamond <http://ab.inf.uni-tuebingen.de/software/diamond/>`_ Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. *Nature Methods* 12: 59–60 doi:10.1038/nmeth.3176.
        
        * `krona <http://sourceforge.net/p/krona/home/krona/>`_ Ondov BD, Bergman NH, and Phillippy AM. 2011. Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12: 385.
        
        
        Cite
        ----
        
        If you find this package useful, please cite this git repository (https://github.com/dparks1134/refinem)
        
        
        Copyright
        ---------
        
        Copyright © 2015 Donovan Parks. See LICENSE for further details.
        
Platform: UNKNOWN
