Supporting data for "Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacbio Sequel II system and ultralong reads of Oxford Nanopore"

The availability of reference genomes has revolutionized the study of biology. Multiple competing technologies have been developed to improve the quality and robustness of genome assemblies during the last decade. The two widely-used long-read sequencing providers Pacbio (PB) and Oxford Nanopore Technologies (ONT) have recently updated their platforms: PB enables high throughput HiFi reads with baselevel resolution with >99% and ONT generated reads as long as 2 Mb. We applied the two up-to-date platforms to one single rice individual and then compared the two assemblies to investigate the advantages and limitations of each. The results showed that ONT ultralong reads delivered higher contiguity producing a total of 18 contigs of which ten were assembled into a single chromosome compared to that of 394 contigs and three chromosome-level contigs for the PB assembly. The ONT ultralong reads also prevented assembly errors caused by long repetitive regions for which we observed a total of 44 genes of false redundancies and ten genes of false losses in the PB assembly leading to over/under-estimation of the gene families in those long repetitive regions. We also noted that the PB HiFi reads generated assemblies with considerably fewer errors at the level of single nucleotide and small InDels than that of the ONT assembly which generated an average 1.06 errors per Kb and finally engendered 1,475 incorrect gene annotations via altered or truncated protein predictions.