Haoyu Cheng from Yale University spoke at London Calling 2025 on “Efficient telomere-to-telomere genome assembly with nanopore reads using hifiasm.”Cheng described the challenges of assembling a diploid human genome. In 2022, the first telomere-to-telomere (T2T) human genome was published. One current strategy is to use long-read data and phasing. There are computational challenges. Hifiasm is […]
Tonight, I started watching the Oxford Nanopore Technologies webinar on September 11, 2024. The title was “Unlocking comprehensive genomes for large-scale projects.” Dr. Karen Stewart moderated the event. Cora Vacher, Associate Director of Segment Marketing – Human Genetics with ONT, began by introducing “the era of complete genomes.” They spoke about the importance of Nanopore ultra-long reads […]
Tonight I started watching a longer session from Oxford Nanopore Technologies (ONT) summer programming. “The era of complete genomes, at any scale” was the title of a session Cora Vaher gave. They described how long-read sequencing with ONT has changed sequencing. Vaher stated that “the era of full genomes is coming” because there are many […]
Temitayo A. Olagunju from the University of Idaho presented at London Calling 2024 on “Assembling a T2T cattle genome with Oxford Nanopore reads.”The breed of cattle they focused on is the gyr, with a characteristic hum on the back and important for milk production. They are often intercrossed/interbred with other bos cattle for their features […]
We had a productive and fun day working in Minneapolis on the PALM and Vision and Change project! I am glad I was able to come here and work with friends. Tonight, I watched the London Calling 2024 session “Plant T2T genome assembly using ultra-long and adaptive nanopore sequencing” by Bosheng Li from the Institute […]
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 […]
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 […]
Alaina Shumate from Johns Hopkins University was a speaker at the Nanopore Community Meeting 2021. Shumate was a graduate student and worked on “The annotation of novel genes in a complete human genome.” They noted that in 2003, scientists “finished” the human genome, but reions were still incomplete. In 2021, the Telomere-to-Telomere (T2T) Consortium was […]
Tonight I watched the NCM Houston Update from Sissel Juul from Oxford Nanopore Technologies. The session is entitled “Covering all bases,” and Juul is the director of the applications team. The talk focused on variant calling mostly on the PromethION. About a year and a half ago, the telomere-to-telomere consortium published the T2T assembly in […]
Tonight I started the Human Genome Sequencing and Analysis Nanopore Learning course. Bala Periaswamy from ONT spoke about using Nanopore sequencing for human genomics. They noted that the long reads can be used to sequence larger portions to analyze human genome variations and epigenomics. They noted that kit 14 along with flow cells and motor […]