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GenGraph: a python module for the simple generation and manipulation of genome graphs.

Jon Mitchell Ambler1, Shandukani Mulaudzi2, Nicola Mulder2

  • 1Wellcome Centre for Infectious Diseases Research in Africa and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town, 7700, South Africa. Jon.Ambler@uct.ac.za.

BMC Bioinformatics
|October 27, 2019
PubMed
Summary
This summary is machine-generated.

GenGraph offers a Python toolkit for creating genome graphs, simplifying complex genomic data representation. This approach overcomes limitations of single reference genomes, aiding researchers in genomics studies.

Keywords:
GenomeGraphModulePythonToolkit

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The limitations of single reference genomes in genomics studies are increasingly apparent with advancements in sequencing technology.
  • Representing collections of genomes as a single genome graph offers a promising solution to this challenge.
  • Existing tools for genome graph creation exist, but there is a need for more flexible research tools.

Purpose of the Study:

  • To present GenGraph, a Python toolkit for generating genome graphs.
  • To provide researchers with flexible tools to overcome challenges in genomics studies.
  • To facilitate experimentation and development of new tools utilizing genome graphs.

Main Methods:

  • GenGraph utilizes existing multiple sequence alignment tools to construct genome graphs.
  • The toolkit employs an intuitive conceptual model where graph structure reflects biological relationships.
  • It leverages existing file formats and methods for graph generation.

Main Results:

  • GenGraph enables the creation of genome graphs from collections of sequences.
  • The toolkit is implemented in Python, a widely used language in biological sciences.
  • Generated graphs can be visualized and imported using common applications like Cytoscape, R, and JavaScript.

Conclusions:

  • GenGraph provides accessible tools for generating graph-based sequence representations.
  • The toolkit features a simple conceptual model and is written in Python.
  • GenGraph is publicly available on Github for researchers.