{ "info": { "author": "Darrin Lemmer", "author_email": "dlemmer@tgen.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "Natural Language :: English", "Operating System :: POSIX", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": ".. image:: https://landscape.io/github/TGenNorth/NASP/tests/landscape.svg?style=flat\n :target: https://landscape.io/github/TGenNorth/NASP/tests\n :alt: Code Health\n\n.. |copy| unicode:: U+000A9 .. COPYRIGHT SIGN\n\nThe Northern Arizona SNP Pipeline (NASP)\n========================================\n\nOVERVIEW:\n---------\n\nNASP is a pipeline for analysis of genomic data. It is a suite of tools\nmeant to collect and report on statistically-relevant high-confidence\npositions in a collection of genomes, with emphasis on variant\npositions, especially single nucleotide polymorphisms (SNPs). NASP\nexpects some combination of files in FASTA, FASTQ, SAM, BAM, and VCF\nformat as input, and will produce output files also in\nthose formats. As NASP is a pipeline, it expects to link a set of\nexternal tools (usually installed separately) to complete specific\nanalysis tasks.\n\nUSAGE:\n------\n\nUsage depends upon the installation method used on your system, and the\nuser interface you select. For standard installations with the\ncommand-line interface, you would collect (or symbolically link) all of\nyour input files into a folder, and then invoke the command-line\ninterface from that folder. Expected usage for the command-line\ninterface is:\n\n`nasp.py [output\\_folder]`\n\nYou will then be prompted to answer a few questions about your analysis.\n\nOptionally, if you are re-running a previous analysis with the same (or\nsimilar) options, you can pass in an xml-based configuration file (this\nis written out to your output\\_folder after running the command-line\ninterface) using the format:\n\n`nasp.py --config`\n\nINSTALLATION:\n-------------\n\nSee the main page for documentation (http://tgennorth.github.io/NASP/).\n\nDEPENDENCIES:\n-------------\n\nFor information about external tools that are required, or can be\nutilized, and those versions that have been tested to work with NASP,\nrefer to the main NASP page (http://tgennorth.github.io/NASP/)\n\nLICENSE:\n--------\n\nCopyright |copy| The Translational Genomics Research Institute See the\nincluded \"LICENSE\" document.\n\nPUBLICATION:\n--------\n\nPlease read our paper for more information:\n\nJason 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\n\n\"NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats\". 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