{
    "info": {
        "author": "Donovan Parks",
        "author_email": "donovan.parks@gmail.com",
        "bugtrack_url": null,
        "classifiers": [],
        "description": "# CleanM\n\n<b>[This project is in active development and not currently recommended for public use.]</b>\n\nCleaM 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. CleanM 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:\n\n<i>Improve completeness:</i>\n* identify contigs with homology to closely related reference genome(s)\n* identify contigs with compatible GC, coverage, and tetranucleotide signatures\n* indetify partial population genomes which should be merged together (requires[CheckM](https://github.com/Ecogenomics/CheckM/wiki))\n\n<i>Reducing contamination:</i>\n* taxonomically classify contigs within a genome in order to identify outliers\n* identify contigs with divergent GC content, coverage, or tetranucleotide signatures\n* identify contigs with a coding density suggestive of a Eukaryotic origin\n\n## Install\n\nThe simplest way to install this package is through pip:\n> sudo pip install cleanm\n\nThis package requires numpy to be installed and makes use of the follow bioinformatic packages:\n\nCheckM relies on several other software packages:\n\n* [prodigal](http://prodigal.ornl.gov/): Hyatt D, Locascio PF, Hauser LJ, Uberbacher EC. 2012. Gene and translation initiation site prediction in metagenomic sequences. <i>Bioinformatics</i> 28: 2223-2230.\n* [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. <i>BMC Bioinformatics</i> 10:421: doi: 10.1186/1471-2105-10-421.\n* [diamond](http://ab.inf.uni-tuebingen.de/software/diamond/) Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. <i>Nature Methods</i> 12: 59\u201360 doi:10.1038/nmeth.3176.\n\n## Cite\n\nIf you find this package useful, please cite this git repository (https://github.com/dparks1134/CleanM)\n\n## Copyright\n\nCopyright \u00a9 2015 Donovan Parks. See LICENSE for further details.",
        "description_content_type": null,
        "docs_url": null,
        "download_url": "UNKNOWN",
        "downloads": {
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            "last_month": -1,
            "last_week": -1
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        "home_page": "http://pypi.python.org/pypi/comparem/",
        "keywords": null,
        "license": "GPL3",
        "maintainer": null,
        "maintainer_email": null,
        "name": "cleanm",
        "package_url": "https://pypi.org/project/cleanm/",
        "platform": "UNKNOWN",
        "project_url": "https://pypi.org/project/cleanm/",
        "project_urls": {
            "Download": "UNKNOWN",
            "Homepage": "http://pypi.python.org/pypi/comparem/"
        },
        "release_url": "https://pypi.org/project/cleanm/0.0.1/",
        "requires_dist": null,
        "requires_python": null,
        "summary": "A toolbox for improving population genomes.",
        "version": "0.0.1"
    },
    "last_serial": 1447068,
    "releases": {
        "0.0.1": []
    },
    "urls": []
}