LSD-Bubble 2.0

Detect all superbubbles in a graph.

Linear Superbubble Detector

Introduction

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

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

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 and the algorithm that it should use:

lsd d path

If you want other detection algorithm try:

lsd p path

or

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