Bosheng Li from the Institute of Advanced Agricultural Sciences of Peking University in China presented at London Calling 2024. The session’s title was “Plant T2T genome assembly using ultra-long and adaptive nanopore sequencing.” They spoke about the importance of ultra-long reads. These reads produce N50 length >100 kb. These are crucial in the assembly of […]
Matthew Jones from Stanford University presented at London Calling 2024 a session titled “CoRAL accurately resolves extrachromosomal DNA structures with long-read sequencing.” This toolkit can be used to study extrachromosomal or ecDNA, a form of oncogene amplification in cancers. ecDNA is not found in normal cells, is associated with shorter patient survival, and is large: […]
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 […]
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 […]
Tonight, I watched the London Calling 2019 session “Ultra-long reads and ultra-long duplications: deciphering the mysteries of the Bordetella pertussis genome.” Natalie Ring from the University of Bath in the UK was the presenter. They spoke about whooping cough and how the introduction of vaccination in the 1950s reduced the number of reported cases. In […]
Nadie Holmes from the University of Nottingham in the UK presented at London Calling 2019 on “Extracting megabase DNA.” They work with DeepSeq providing training and core sequencing support. Holmes worked on collaborative projects to optimize ultra-long sequencing. They shared data from a 1.3 megabase read. They use the protocol developed by Josh Quick to […]
I have been reading about the Ultra-long Sequencing Kit from Nanopore to try it this summer. Tonight I found the Ultra-long Reads YouTube playlist from ONT. I watched the session by Jillian Hammond from the Garvan Institute of Medical Research in Australia. They presented on the use of Ultra-long Reads for Australian Reptiles. They noted […]
The Nanopore Learning course on Human genome sequencing and analysis has a video on the Kit V14 performance. Vania Costa, a member of Oxford Nanopore Technologies Technical Services Team, explained how kit 14 uses R10.4.1 flow cells for increased simplex Q20+ accuracy and duplex Q30+ accuracy. The R9 kit will be discontinued at the end […]
The Nanopore Learning course on “Human genome sequencing and analysis” has a video on Kit V14. Vania Costa, a Technical Services Specialist with Oxford Nanopore Technologies, described the accuracy of kit 14, which relies on R10.4.1 flow cells and pores. Costa explained that kit v14 has simplex Q20+ and duplex Q30+. Currently, there are ligation-based […]
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 […]