Metadata-Version: 1.1
Name: ragout
Version: 0.2b
Summary: A tool for reference-assisted assembly
Home-page: http://github.com/fenderglass/Ragout
Author: Mikhail Kolmogorov
Author-email: fenderglass@gmail.com
License: GPLv2
Description: Ragout
        ======
        
        Version: 0.2 beta
        
        Release date: 15 Apr 2014
        
        
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        Description
        -----------
        Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
        assisted assembly using multiple references. It takes a short read
        assembly (a set of contigs), a set of related references
        and a corresponding phylogenetic tree and then assembles the contigs into
        scaffolds.
        
        The benefits of assembly with multiple references become significant,
        when those references have structural variations compared to the target
        genome. Even if each reference is structurally divergent, it is possible
        to assemble the target into the correct set of scaffolds. Enlarge your
        contigs with Ragout!
        
        The current version of Ragout is limited to genomes of bacterial size,
        but we are working on expanding it to mammalian-scaled ones.
        
        
        Install
        -------
        See *docs/INSTALL.md* file.
        
        Usage
        -----
        See *docs/USAGE.md* file.
        
        
        Authors
        -------
        - Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of
        Sciences)
        - Son Pham (University of California, San Diego)
        
        
        Citation
        --------
        - Mikhail Kolmogorov, Brian Raney, Benedict Paten, and Son Pham. 
        "Ragout: A reference-assisted assemble tool for bacterial genomes" 
        (accepted to ISMB 2014)
        
        
        ISMB 2014 supplementary
        -----------------------
        
        Supplementary materials for ISMB submission could be found at:
        https://drive.google.com/file/d/0B1pUguR1yn7TMjNpX09JdFphT3c/edit?usp=sharing
        
        
        Contacts
        --------
        Please report any bugs directly to the issue tracker of this project.
        Also, you can send your feedback at fenderglass@gmail.com
        
        
        Acknowledgements
        ----------------
        The work was supported by VP Foundation.
        
        We would like to thank:
        - Nikolay Vyahhi (testing and some useful suggestions)
        - Aleksey Gurevich (testing)
        
        
        Licence
        -------
        The program is distributed under GNU GPL v2 license.
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: POSIX
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Classifier: Programming Language :: Python
Classifier: Programming Language :: C++
