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Detect all superbubbles in a graph.

Project description

Linear Superbubble Detector


This project gives the reference implementation of the Linear Superbubble Dector (LSD).


  • 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


The documentation can be found at:


The simples way to install is using pip:

pip install LSD-Bubble

You can also download the source from and run the make script to install the package. These needs that setuptools are installed.


The programms needs only a path to a graph file to work and the algorithm that it should use:

lsd d path

If you want other detection algorithm try:

lsd p path


lsd o path

If as input format not edgelist is used give the format with the -f parameter

lsd d path -f gml

If you want a different reporting format use -r

lsd d path -r count

If you want not to detect superbubbles but week superbubbles use –week:

lsd d path –week

Project details

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Files for LSD-Bubble, version 2.0
Filename, size File type Python version Upload date Hashes
Filename, size LSD_Bubble-2.0-py3.7.egg (88.6 kB) File type Egg Python version 3.7 Upload date Hashes View
Filename, size LSD_Bubble-2.0-py3-none-any.whl (36.0 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size LSD-Bubble-2.0.tar.gz (16.1 kB) File type Source Python version None Upload date Hashes View

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