Metadata-Version: 1.1
Name: swga
Version: 0.4.0
Summary: Pipeline to select compatible primer sets for selective whole-genome amplification.
Home-page: https://github.com/eclarke/swga
Author: Erik Clarke
Author-email: ecl@mail.med.upenn.edu
License: LICENSE.txt
Description: # Selective whole genome amplification
        [![Build Status](https://travis-ci.org/eclarke/swga.svg?branch=master)](https://travis-ci.org/eclarke/swga)
        [![Coverage Status](https://coveralls.io/repos/eclarke/swga/badge.svg?branch=dev&service=github)](https://coveralls.io/github/eclarke/swga)
        ## Introduction 
        This is an easy-to-use, start-to-end package for finding sets of primers that selectively amplify a particular genome (the "foreground" genome) over a background genome. For instance, we can design a set of primers that amplify a parasite's genome in a sample that is overwhelmingly composed of host DNA.
        
        You can run SWGA on hardware ranging from a Mac laptop to a high-end server. 
        
        ## Features:
        - Counts all the possible primers in a size range in both genomes
        - Filters primers based on:
          - foreground and background genome binding rates
          - melting temperatures (with a built-in melt temp calculator that accounts for mono- and divalent cation solutions!)
          - Possible homodimerization
        - Finds primer sets containing primers that are compatible with each other using graph theory (largest clique formation). The process ensures:
          - No primer in a set is a heterodimer
          - Even binding site spacing in foreground genome
          - Low total binding to background genome
        - Score each set based on certain binding metrics and allows exploration of high-scoring sets via output to common formats.
        
        ## Installation
        Follow the installation instructions [here](https://github.com/eclarke/swga/wiki/Installation)
        
        ## Using SWGA
        Follow the guide on our Wiki/[Quick Start](https://github.com/eclarke/swga/wiki/Quick-Start) to get started!
        
        ## Updates
        New features and bugfixes are released all the time. To update, simply follow steps 3-5 on the [installation instructions](https://github.com/eclarke/swga/wiki/Installation).
        
        ## 3rd-party code
        SWGA incorporates code from other open-source projects:
        - `cliquer`, a clique-finding library by Sampo Niskanen and Patric Ostergard
             - http://users.aalto.fi/~pat/cliquer.html
        - `DSK`, a disk-based kmer-counting tool by G. Rizk
             - http://minia.genouest.org/dsk/
             - Citation: (Rizk, G., Lavenier, D. and Chikhi, R. DSK: k-mer counting with very low memory usage, Bioinformatics, 2013.)
        
        Cliquer is copyright © 2002 Sampo Niskanen, Patric Östergård. and licensed under the GPL.
        
        DSK is licensed under the CeCILL license, which can be found in src/dsk/LICENSE, and is GPL compatible.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
