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.
Documentation is available on Read The Docs. Documentation can be locally built under docs folder
using sphinx. sphinx is automatically installed when installing gaftools in dev mode.
Preprint 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.