Dr. Sergey Koren from the National Institutes of Health presented at London Calling 2023 on “Automated telomere-to-telomere crop genome assembly using only Oxford Nanopore sequencing.” His background is in computer science. Dr. Koren began by mentioning that the telomere-to-telomere (T2T) human genome was recently completed, adding almost 8-10% to the genome. He described how Nanopore duplex sequencing has been improving. The throughput varied, with flow cells from early 2023 producing 20 Gbases. The length of ONT reads with duplex sequencing for the tomato genome was demonstrated, showing impressive lengths and improved quality. Their longest read was 187 Kb, with a quality score of Q31! Bandage plots indicated that most of the assemblies were telomere-to-telomere with the help of Verko. Dr. Koren compared the results of PacBio HiFi and ONT duplex sequencing. Both techniques achieved telomere-to-telomere assemblies, with some heterozygosity and gaps in both cases. ONT duplex sequencing produced robust assemblies with some manual refining and ultra-long reads to resolve gaps. Dr. Koren emphasized that both HiFi and ONT duplex sequences have their advantages and drawbacks for genome assemblies. They also highlighted the importance of validating assemblies and identifying any issues. Furthermore, assemblies were improved using DeepConsensus from Google! Dr. Koren mentioned that the new flow cells will further enhance ONT duplex sequencing throughput and quality. It would be exciting to try those flow cells!
