We often use Oxford nanopore reads for de novo assembly of genomes and plasmids. Sean Mckenzie, Associate Director of Genomic Applications Bioinformatics with Oxford Nanopore Technologies, provided an update on assembly performance. They described de novo assembly as “the process of reconstructing an organism’s genome sequence from a set of genomic sequencing reads.” There are many tools for assembly. For human telomere-to-telomere (T2T) assembly, the ONT team developed a protocol for T2T. The ONT team generated 45X ultra-long data (N50= 100 kbp) basecalled with Dorado SUP V5 models. The human genome reads were pre-corrected with Dorado correct and assembled with the Verkko pipeline (35X pore-c used for graph phasing). The final assembly was 30 T2T contigs + 5 T2T scaffolds with an N50 of 144/147 Mbp. Mckenzie noted that they will release a polishing kit (Assembly Polishing Kit, APK) using 6b4 technology. Medaka polished T2T assembly with 35X APK produced a polished Q accuracy of 51! The ONT team is developing a high-quality assembly pipeline from standard LSK output. They used this tool to assemble the haploid genome of the honeybee. This tool uses hifiasm and may be integrated with Dorado. I am excited to learn more about this tool and how we can use it to assemble waxworm genomes with standard LSK data.
