Metadata-Version: 2.4
Name: gaftools
Version: 1.1.3
Summary: Toolkit for pangenome alignments
Author: Arda Soylev, Fawaz Dabbaghie, Tobias Marschall
Author-email: Samarendra Pani <samarendra.pani@hhu.de>
Maintainer-email: Samarendra Pani <samarendra.pani@hhu.de>
License-Expression: MIT
Project-URL: Homepage, https://github.com/marschall-lab/gaftools
Project-URL: Issues, https://github.com/marschall-lab/gaftools/issues
Project-URL: Changelog, https://github.com/marschall-lab/gaftools/blob/main/CHANGES.rst
Keywords: bioinformatics,genomics,pangenome,toolkit
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: pysam
Requires-Dist: pywfa==0.5.1
Provides-Extra: dev
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Requires-Dist: tox; extra == "dev"
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Requires-Dist: sphinx-rtd-theme; extra == "dev"
Requires-Dist: sphinx-better-subsection; extra == "dev"
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Provides-Extra: docs
Requires-Dist: sphinx; extra == "docs"
Requires-Dist: sphinx-rtd-theme; extra == "docs"
Requires-Dist: sphinx-issues; extra == "docs"
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Dynamic: license-file
Dynamic: requires-dist

.. image:: https://img.shields.io/pypi/v/gaftools.svg?branch=main
    :target: https://pypi.python.org/pypi/gaftools

.. image:: https://github.com/marschall-lab/gaftools/workflows/CI/badge.svg


gaftools
========

gaftools is a fast and comprehensive toolkit designed for processing pangenome alignments. It provides various functionalities such as
indexing, sorting, realignment, viewing and statistical analysis of rGFA-based GAF files.

`Link to GitHub <https://github.com/marschall-lab/gaftools/tree/main>`_

`Documentation <https://gaftools.readthedocs.io/>`_ is available on Read The Docs. Documentation can be locally built under :code:`docs` folder
using :code:`sphinx`. :code:`sphinx` is automatically installed when installing gaftools in `dev` mode.

`Preprint <https://www.biorxiv.org/content/10.1101/2024.12.10.627813v1>`_ is available on bioRxiv.

Features
--------

* Viewing GAF files based on user-defined regions or node IDs.
* Conversion of GAF format from unstable segment coordinates to stable coordinates and vice-versa.
* New tags for GFA files for ordering of bubbles and sorting GAF files.
* Post-processing GAF alignments using Wavefront Alignment and generating basic alignment statistics.
* Easy-to-install. Available in PyPI and bioconda.
* Open Source (MIT License)

Citation
--------

Pani, S., Dabbaghie, F., Marschall, T. & Söylev, A. gaftools: a toolkit for analyzing and manipulating pangenome alignments. (2024) doi:10.1101/2024.12.10.627813.
