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An experimental python wrapper for gatb-core

Project description

License: Affero-GPL Platform: C++11 Python3 Run on Linux-Mac OSX

MacOSX Linux
Build Status OSX Build Status Ubuntu

About pyGATB

pyGATB is a Python3 wrapper for the GATB-Core library.

The current release of pyGATB gives access to the following GATB-Core components:

  • Bank: the class that enables to load Fasta and Fastaq files
  • Sequence: the class that holds a sequence (ID, letters, quality)
  • Graph: the class that holds the De Bruijn graph
  • Node: the class that makes graph’s nodes

Using that API you can start prototyping algorithms:

  • read a sequence file (Bank): FastA, FastQ (plain text or gzipped)
  • or read a set of files (still using the same Bank!)
  • convert that Bank to a De Bruijn graph (Graph)
  • navigate through the Graph (Node)

all of that directly using the Python Programming Language.


Jump to the wiki to review how to install, use and make pyGATB Python3 compliant codes.


pyGATB and GATB-Core are free softwares; you can redistribute it and/or modify it under the Affero GPL v3 license.

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