Metadata-Version: 1.0
Name: capsid
Version: 1.2.6
Summary: CaPSID: Computational Pathogen Sequence Identification
Home-page: https://github.com/capsid/capsid
Author: Shane Wilson
Author-email: shane.wilson@oicr.on.ca
License: GNU General Public License, Version 3.0
Download-URL: https://github.com/capsid/capsid
Description: CaPSID
        ========
        **CaPSID** (Computational Pathogen Sequence IDentification) is a comprehensive open source platform which integrates a high-performance computational pipeline for pathogen sequence identification and characterization in human genomes and transcriptomes together with a scalable results database and a user-friendly web-based software application for managing, querying and visualizing results.
        
        **Project Leader** Vincent Ferretti  
        **Development Team** Ivan Borozan, Philippe Laflamme, Shane Wilson
        
        Downloading and using CaPSID is free, if you use CaPSID or its code in your work 
        please acknowledge CaPSID by referring to its github homepage https://github.com/capsid. 
        This is important for us since obtaining grants is one significant way to fund planning 
        and implementation for our project. Also if you find CaPSID useful in your research feel 
        free to let us know.  
        
        Getting Started
        ---------------
        You will need a MongoDB database, a Python 2.7 installation and a Java Web Server. For more details, read the wiki:
        
          https://github.com/capsid/capsid/wiki/
        
        License and Copyright
        ---------------------
        Licensed under the GNU General Public License, Version 3.0. See LICENSE for more details.
        
        Copyright 2011 The Ontario Institute for Cancer Research.
        
        Acknowledgement
        ---------------
        This project is supported by the Ontario Institute for Cancer Research
        (OICR) through funding provided by the government of Ontario, Canada.
        
        
        News
        ====
        
        1.2.6
        -----
        
        *Release date: 6 Feb 2012*
        
        * Subtraction filters out unmapped when building mapped reads
        
        1.2
        ---
        
        *Release date: 20 Jan 2012*
        
        * Utility to create FastQ files from unmapped reads
        * Utility to return intersection of FastQ files
        * Utility to return filter FastQ files
        * Added mapq threshold flag to subtraction
        * Gbloader can now load bacteria and fungal genomes
        * Saves genome sequences to database using GridFS
        * Reduced memory footprint when calculating statistics
        * use subprocesses instead of os.system
        * mapq scores filter needs to include 0 <= mapq <=3 due to multiple mapping reads
        
        1.1
        ---
        
        *Release date: 25 Nov 2011*
        
        * Adds support for pair-end reads
        
        1.0.1
        -----
        
        *Release date: 19 Oct 2011*
        
        * Added support for MongoDB authentication
        
        1.0
        ---
        
        *Release date: 12 Oct 2011*
        
        * Initial release
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: Unix
