: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events.

The use of -mers to capture genetic variation in bacterial genome-wide association studies (bGWAS) has demonstrated its effectiveness in overcoming the plasticity of bacterial genomes by providing a comprehensive array of genetic variants in a genome set that is not confined to a single reference genome. However, little attempt has been made to interpret -mers in the context of genome rearrangements, partly due to challenges in the exhaustive and high-throughput identification of genome structure and individual rearrangement events. Here, we present , a pre- and post-bGWAS processing methodology that leverages the unique properties of -mers to facilitate bGWAS for genome rearrangements. Repeat sequences are common instigators of genome rearrangements through intragenomic homologous recombination, and they are commonly found at rearrangement boundaries. Using whole-genome sequences, repeat sequences are replaced by short placeholder sequences, allowing the regions flanking repeats to be incorporated into relatively short -mers. Then, locations of flanking regions in significant -mers are mapped back to complete genome sequences to visualise genome rearrangements. Four case studies based on two bacterial species ( and ) and a simulated genome set are presented to demonstrate the ability to identify phenotype-associated rearrangements. is available at https://github.com/DorothyTamYiLing/GWarrange.