Nanopore-only genome assemblies of Arabidopsis thaliana Col-0 across sequencing chemistries, basecalling models, and assembly workflows

This dataset contains 20 de novo genome assemblies of Arabidopsis thaliana Columbia (Col-0) generated exclusively from Oxford Nanopore Technologies long-read sequencing. The assemblies were generated from three sequencing runs representing successive nanopore chemistries: ATRun1: R9.4.1 flow cell and SQK-LSK109 library ATRun2: R10.4 flow cell and SQK-Q20EA library ATRun3: R10.4.1 flow cell and SQK-LSK114 library ATRun1 and ATRun2 reads were assembled using Canu, Flye, Miniasm, wtdbg2, and the ONT Pomoxis pipeline. Assemblies are provided for both the original high-accuracy (HAC) basecalls and super-accuracy (SUP) rebasecalls where available. The Canu, Flye, Miniasm, and wtdbg2 assemblies were polished using Racon and Nanopolish, while the Pomoxis assemblies were polished using Medaka. ATRun3 SUP reads were assembled using hifiasm in ONT mode. The deposited ATRun3 assembly is a curated nuclear assembly consisting of five contigs corresponding to the five A. thaliana nuclear chromosomes. Low-coverage and organellar contigs were excluded. The assembly has a total length of 134.93 Mb, an N50 of 26.15 Mb, 99.9% complete BUSCOs, and an estimated consensus QV of 68.85. Files are provided as gzip-compressed, unannotated FASTA files. Raw sequencing data and associated assemblies are also linked to European Nucleotide Archive project PRJEB79853.