This dataset contains supporting files referenced by the following publication: • Rabanal FA, Gräff M, Lanz C, Fritschi K, Llaca V, Lang M, Carbonell-Bejerano P, Henderson I, Weigel D. Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes. Nucleic Acids Research. doi: 10.1093/nar/gkac1115 Directory structure: Bionano_optical_maps_based_assemblies: this directory contains results from the Bionano optical map based scaffolding for the main long-read assemblers analysed in the study for Arabidopsis thaliana accession Ey15-2 (9994): 9994.CLR_Canu 9994.HiFi_FALCON 9994.HiFi_HiCanu 9994.HiFi_Hifiasm 9994.HiFi_IPA 9994.HiFi_Peregrine Col-0_HiFi-Hifiasm_assembly: this directory contains the Pacbio HiFi based chromosome level assembly (fasta file) and repeat annotation (gff file) of Arabidopsis thaliana accession Col-0 (6909). Ey15-2_HiFi-Hifiasm_plus_CLR-Canu_assembly: this directory contains the Pacbio HiFi+CLR based chromosome level assembly (fasta file) and repeat annotation (gff file) of Arabidopsis thaliana accession Ey15-2 (9994). Naish2021_Wang2021_repeat_annotation: this directory contains the repeat annotation (gff files) for the Arabidopsis thaliana Col-0 (6909) assemblies performed by Naish et al. (doi: 10.1126/science.abi7489) and Wang et al. (doi: 10.1016/j.gpb.2021.08.003). TAIR10_masked: this directory contains the repeat-hard-masked version of the TAIR10 Arabidopsis thaliana Col-0 (6909) reference genome that was used for in silico scaffolding of contigs with RagTag (https://github.com/malonge/RagTag).