Telomere-to-telomere assembly has been coming up in Nanopore Community Meeting 2022 sessions frequently. The session I watched tonight had it in the title: “Expanding studies of global genomic diversity with complete, telomere-to-telomere assembly of diploid genomes” presented by Karen Miga from the University of California, Santa Cruz. Miga shared information about the release of the telomere-to-telomere human genome. I did not realize that “nearly 200 Mb of new sequence” were generated to close gaps. Miga shared an image of the cover of Science, and note that what we learned was that quality matters. Having complete assemblies with PacBio HiFi and ONT long-reads helps provide more accurate gene counts. Miga noted that this is very important for comprehensive analysis, including methylation and variation. Miga spoke how difficult it was to analyze the Y chromosome, and now it has been sequenced telomere-to-telomere “T2T.” Miga spoke that new technologies will be needed to continue with the T2T movement for reference genomes. Miga focused on the efforts of the Human Pangenome Reference Consortium to “improve representation of global diversity (>350 diverse diploid references)” and “…aim to release a complete (T2T) and comprehensive map of genome variation.” Miga highlighted that this is a multicenter effort with PacBio, ONT, and Omni-C. The T2T Consortium “aims to release a highly accurate (Q100) reference”! Miga’s wishlist included longer Q30 reads… and they already began using PromethION with stereo duplex reads! The team has been using these early access reagents to produce Q30.1 and duplex (as well as single strand) data. I had heard about this and finally saw the data in Miga’s presentation! Miga also spoke about PoreC and a GFAse “phasing graphs with proximity linkage data” method. This method and others, Miga thinks, will help reduce the per genome cost to reach T2T. Miga acknowledged the T2T Consortium and numerous partners involved in this massive project. I now have to follow their work to learn of new approaches that will, as Miga says, “T2T under one roof.”
