Metadata-Version: 1.1
Name: LSD-Bubble
Version: 1.0
Summary: Detect all superbubbles in a graph.
Home-page: https://github.com/Fabianexe/Superbubble
Author: Fabian Gaertner
Author-email: fabian@bioinf.uni-leipzig.de
License: BSD 3-Clause
Description: Linear Superbubble Detector
        ===========================
        
        .. image:: https://raw.githubusercontent.com/Fabianexe/Superbubble/master/logo.png
        
        Introduction
        ------------
        This project gives the reference implementation of the Linear Superbubble Dector (LSD).
        
        .. _`NetworkX`: https://networkx.github.io
        .. _`NetworkX can load`: https://networkx.github.io/documentation/stable/reference/readwrite/index.html
        
        Features
        --------
        - Detect superbubbles in linear time
        - Uses `NetworkX`_  as graph library
        - Can load plenty file formats (everything that `NetworkX can load`_ )
        - Have different ways to report the superbubbles
        - Simple and clean code
        - Simple to understand and reimplement
        
        Documentation
        =============
        The documentation can be found at:
        https://fabianexe.github.io/Superbubble
        
        Installation
        ------------
        The simples way to install is using pip::
        
           pip install LSD-Bubble
        
        .. _`setuptools`: https://pypi.python.org/pypi/setuptools
        
        You can also download the source from https://github.com/Fabianexe/Superbubble and run the make script to install the package.
        These needs that `setuptools`_ are installed.
        
        Usage
        -----
        The programms needs only a path to a graph file to work:
        
           lsd *path*
        
        If as input format not edgelist is used give the format with the -f parameter
        
           lsd *path* -f gml
        
        If you want a different reporting format use -r
        
           lsd *path* -r count
        
        If you want not to detect superbubbles but week superbubbles use --week:
        
           lsd *path* --week
        
Keywords: graph,superbubble,﻿de Bruijn graph,﻿Genome assembly,﻿Linear time algorithm
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
