Sissel Juul, Vice President of Applications with Oxford Nanopore Technology and Sean McKenzie, Associate Director of Genomics Applications, provided the London Calling 2025 applications update. Juul explained that the applications team is global. Haplotype-resolved genetic variation detection and interpretation has been updated to use assembly approaches. However, assembly can be very challenging, especially with two very similar genomes or complex mixtures. McKenzie spoke about about the assembly of prokaryotes The NO-MISS protocol and autocycler have improved isolate assembly. Raw consensus accuracy has improved with the majority of organisms with a consensus accuracy above Q50. The NanoMDBG assembler for nanopore metagenomic data was used to sequence the ZymoBIOMICS fecal reference. With 200Gb per flow cell, the data produced excellent quality MAGs. A compost sample was sequenced on eight PromethION flow cells, resulting in 1.17 Tb of data and producing 5,598 MQ+ MAGs. McKenzie also described the power of reference-based human variant analyses. The new best Nanopore-only assembly of the human genomes has also been improved. Hifiasm from Oxford Nanopore Technologies (ONT) increases speed for near T2T assembly. This assembler is working well for genomes from plants and animals and works with both ultra-long and ligation-based sequencing libraries. McKenzie did note that you need long-range phasing information for the assembler to produce best data. McKenzie then shared several examples of the use of ONT for resolving challenging clinically relevant regions. Juul shared that LSK and Pore-C libraries were sequenced on a single flow cell (high capacity) that was completely phased. Juul emphasized that assemblies with Nanopore sequencing continue to improve.
