Karen Miga from the University of California, Santa Cruz, presented at London Calling 2019 on “Telomere-to-telomere assembly of a complete human X chromosome.” Miga is part of the Telomere-to-Telomere Consortium. They spoke about the gaps in the human genome. The challenge of assembling repeat regions may be tackled with ultra-long reads. Using the Josh Quick protocol for ultra-long sequencing, the team has generated 30X Nanopore sequencing in addition to PacBio and short reads. CHM13 was assembled with Canu. They first focused on chromosome X. Number of repeats was validated with digital droplet PCR, and BioNano was used for quality control. Beth Sullivan from Duke helped verify the structure through digestion and pulse field gel electrophoresis. After structural validation, the team took on polishing the assembly. HiFi alignments were used to evaluate the multi-step polishing. The structurally validated array served as a framework or protocol for sequencing other chromosomes and satellites. While the team polishes other regions, they also use high-resolution sequence maps of the centromeric regions with microscopy. At the time of the presentation, the goal was to complete sequencing by automating the process as much as possible. The consortium focused on long-read sequencing and cloud-based assemblies. I enjoyed learning about the process and history of the work of the T2T Consortium!
