Metadata-Version: 1.1
Name: nasp
Version: 1.1.0
Summary: Northern Arizona SNP Pipeline
Home-page: https://github.com/TGenNorth/nasp
Author: Darrin Lemmer
Author-email: dlemmer@tgen.org
License: Academic and Research License
Description: .. image:: https://landscape.io/github/TGenNorth/NASP/tests/landscape.svg?style=flat
           :target: https://landscape.io/github/TGenNorth/NASP/tests
           :alt: Code Health
        
        .. |copy|   unicode:: U+000A9 .. COPYRIGHT SIGN
        
        The Northern Arizona SNP Pipeline (NASP)
        ========================================
        
        OVERVIEW:
        ---------
        
        NASP is a pipeline for analysis of genomic data. It is a suite of tools
        meant to collect and report on statistically-relevant high-confidence
        positions in a collection of genomes, with emphasis on variant
        positions, especially single nucleotide polymorphisms (SNPs). NASP
        expects some combination of files in FASTA, FASTQ, SAM, BAM, and VCF
        format as input, and will produce output files also in
        those formats. As NASP is a pipeline, it expects to link a set of
        external tools (usually installed separately) to complete specific
        analysis tasks.
        
        USAGE:
        ------
        
        Usage depends upon the installation method used on your system, and the
        user interface you select. For standard installations with the
        command-line interface, you would collect (or symbolically link) all of
        your input files into a folder, and then invoke the command-line
        interface from that folder. Expected usage for the command-line
        interface is:
        
        `nasp.py [output\_folder]`
        
        You will then be prompted to answer a few questions about your analysis.
        
        Optionally, if you are re-running a previous analysis with the same (or
        similar) options, you can pass in an xml-based configuration file (this
        is written out to your output\_folder after running the command-line
        interface) using the format:
        
        `nasp.py --config`
        
        INSTALLATION:
        -------------
        
        See the main page for documentation (http://tgennorth.github.io/NASP/).
        
        DEPENDENCIES:
        -------------
        
        For information about external tools that are required, or can be
        utilized, and those versions that have been tested to work with NASP,
        refer to the main NASP page (http://tgennorth.github.io/NASP/)
        
        LICENSE:
        --------
        
        Copyright |copy| The Translational Genomics Research Institute See the
        included "LICENSE" document.
        
        PUBLICATION:
        --------
        
        Please read our paper for more information:
        
        Jason W. Sahl,  Darrin Lemmer,  Jason Travis,  James M. Schupp,  John D. Gillece,  Maliha Aziz,  Elizabeth M. Driebe,  Kevin P. Drees,  Nathan D. Hicks,  Charles Hall Davis Williamson,  Crystal M. Hepp,  David Earl Smith,  Chandler Roe,  David M. Engelthaler,  David M. Wagner, Paul Keim
        
        "NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats". Published Ahead of Print: 21 June, 2016 Microbial Genomics doi: 10.1099/mgen.0.000074 
        (http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000074)
        
        
        CONTACT:
        --------
        
        | TGen North
        | 3051 W Shamrell Blvd Ste 106
        | Flagstaff, AZ 86001-9435
        
        | Darrin Lemmer
        | dlemmer@tgen.org
        | +1-928-226-6374
        
        
        
        
        History
        =======
        
        
        1.0.0 (2014-06-05)
        ------------------
        
        * First release on PyPI.
        
        0.9.6 (2014-06-05)
        ------------------
        
        * First release on PyPI.
        
Keywords: nasp
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
