Minimum virtual dataset for reproducible triploid de novo genome assembly

Despite technological advancements, whole-genome sequencing remains technically challenging for organisms with higher-ploidy genomes. Therefore, the use of short-read sequencing platforms for this purpose has been attempted, but the conditions that result in poor-quality genomes have not been elucidated. Therefore, in the present study, simulated sequences mimicking the accumulation of insertion/deletion mutations were created to clarify the permissible differences between homologous chromosomes and the k-mer sizes for good-quality genome assembly from short-read sequencing data for triploid species. The results illustrated that a narrow range of k-mers permits the generation of high-quality assemblies for any level of difference between homologous chromosomes. This dataset consists of the virtual haploid genome (O.fasta), triploid genome data (reference_sequense), NGS read data (NGS_reads), and assembly results (all_contigs) created in this study.