gaftools: a toolkit for analyzing and manipulating pangenome alignments

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ID: 323042
2026
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Abstract
MOTIVATION: Linear reference genomes are ubiquitously used in genomics research, despite known biases associated with their use. In recent years, there has been a shift towards graph-based reference genomes to address some of these biases, which has required development of new algorithms and file formats. This has created a necessity for new tools capable of utilizing these formats and performing operations similar to those carried out by traditional methods. RESULTS: In this paper we present "gaftools", a multi-purpose tool that introduces several utilities for processing graph alignments in GAF format. Gaftools enables users to index and sort alignments, with graph ordering serving as a necessary step for the sorting process. Additionally, it allows users to view subsets of alignments and perform realignment using the wavefront alignment algorithm, among other features. Many of these functionalities are inspired by SAMtools, which provides similar operations for linear genomes, while gaftools adapts and extends them for pangenomes. AVAILABILITY: gaftools is available under MIT license at https://github.com/marschall-lab/gaftools.
Reference Key
openalex_W4405492923 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Samarendra Pani, Fawaz Dabbaghie, Tobias Marschall, Arda Söylev
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag406
URL
https://doi.org/10.1093/bioinformatics/btag406
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