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

<p>This dataset contains supporting files referenced by the following publication:</p> <p>&bull; Rabanal FA, Gr&auml;ff 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&nbsp;<em>Arabidopsis thaliana</em>&nbsp;genomes</strong>.&nbsp;<em>Nucleic Acids Research</em>. doi: 10.1093/nar/gkac1115</p> <p>&nbsp;</p> <p>Directory structure:</p> <ul> <li><strong>Bionano_optical_maps_based_assemblies</strong>: this directory contains results from the Bionano optical map based scaffolding&nbsp;for the main long-read assemblers analysed in the study for <em>Arabidopsis thaliana</em> accession&nbsp;Ey15-2 (9994): <ul> <li><strong>9994.CLR_Canu</strong></li> <li><strong>9994.HiFi_FALCON</strong></li> <li><strong>9994.HiFi_HiCanu</strong></li> <li><strong>9994.HiFi_Hifiasm</strong></li> <li><strong>9994.HiFi_IPA</strong></li> <li><strong>9994.HiFi_Peregrine</strong></li> </ul> </li> </ul> <p>&nbsp;</p> <ul> <li><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&nbsp;Col-0 (6909).&nbsp;</li> </ul> <p>&nbsp;</p> <ul> <li><strong>Ey15-2_HiFi-Hifiasm_plus_CLR-Canu_assembly</strong>:&nbsp;this directory contains the Pacbio HiFi+CLR based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession&nbsp;Ey15-2 (9994).&nbsp;</li> </ul> <p>&nbsp;</p> <ul> <li><strong>Naish2021_Wang2021_repeat_annotation</strong>: this directory contains the repeat annotation (gff files) for the&nbsp;<em>Arabidopsis thaliana</em>&nbsp;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).&nbsp;</li> </ul> <p>&nbsp;</p> <ul> <li><strong>TAIR10_masked</strong>: this directory contains the repeat-hard-masked version of the TAIR10&nbsp;<em>Arabidopsis thaliana</em>&nbsp;Col-0 (6909) reference genome that was used for in silico scaffolding of contigs with RagTag (<a href="http://github.com/malonge/RagTag">https://github.com/malonge/RagTag</a>).</li> </ul> <p>&nbsp;</p>