Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes"

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. <strong>Pushing the limits of HiFi assemblies reveals centromere diversity between two <em>Arabidopsis thaliana</em> genomes</strong>. <em>Nucleic Acids Research</em>. doi: 10.1093/nar/gkac1115 Directory structure: <strong>Bionano_optical_maps_based_assemblies</strong>: this directory contains results from the Bionano optical map based scaffolding for the main long-read assemblers analysed in the study for <em>Arabidopsis thaliana</em> accession Ey15-2 (9994): <strong>9994.CLR_Canu</strong> <strong>9994.HiFi_FALCON</strong> <strong>9994.HiFi_HiCanu</strong> <strong>9994.HiFi_Hifiasm</strong> <strong>9994.HiFi_IPA</strong> <strong>9994.HiFi_Peregrine</strong> <strong>Col-0_HiFi-Hifiasm_assembly</strong>: this directory contains the Pacbio HiFi based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Col-0 (6909). <strong>Ey15-2_HiFi-Hifiasm_plus_CLR-Canu_assembly</strong>: this directory contains the Pacbio HiFi+CLR based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Ey15-2 (9994). <strong>Naish2021_Wang2021_repeat_annotation</strong>: this directory contains the repeat annotation (gff files) for the <em>Arabidopsis thaliana</em> Col-0 (6909) assemblies performed by Naish <em>et al.</em> (doi: 10.1126/science.abi7489) and Wang <em>et al.</em> (doi: 10.1016/j.gpb.2021.08.003). <strong>TAIR10_masked</strong>: this directory contains the repeat-hard-masked version of the TAIR10 <em>Arabidopsis thaliana</em> Col-0 (6909) reference genome that was used for in silico scaffolding of contigs with RagTag (https://github.com/malonge/RagTag).