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.

Detailed documentation is available here.

The publication is available here.

Citation

Pani, S., Dabbaghie, F., Marschall, T., & Söylev, A. (2026). gaftools: a toolkit for analyzing and manipulating pangenome alignments. Bioinformatics, 42(8). https://doi.org/10.1093/bioinformatics/btag406