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Building pangenome graphs

Please note: As of 1 July 2025, the New Zealand Institute for Public Health and Forensic Science (PHF Science) is the new name for the Institute of Environmental Science and Research (ESR). Research and reports published prior to this date may reference the organisation’s former name.

Abstract

Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships.

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