Mantas Sereika, a Ph.D. student at Aalborg University in Denmark, spoke at the Nanopore Community Meeting 2021 about “Nanopore R10.4 enables near-perfect bacterial genomes.” This topic is of interest for several of the courses I teach. Sereika spoke about the improvements in accuracy of Nanopore sequencing. Raw read accuracy has increased but there are still […]
Andre Sim from the Genome Institute of Singapore (A*STAR) in Singapore spoke at the Nanopore Community Meeting 2021 about “Bambu – generating context-aware transcriptomes with Oxford Nanopore long-reads.” What a cool name! Sim explained that RNA sequencing technologies have evolved, but reference annotation for transcript analysis has remained relatively unchanged. Sim noted that fragments could […]
Tonight I watched the Nanopore Community Meeting 2021 recording featuring Areeba Patel and titled “Rapid-CNS2: rapid, comprehensive adaptive nanopore sequencing of central nervous system (CNS) tumours.” Patel is at the German Cancer Research Center (DKFZ) and the University Hospital Heidelberg, Germany. Patel spoke about the use of molecular diagnostics for CNS tumors. They noted the […]
Miles Benton from the Institute of Environmental Science and Research in New Zealand spoke at the Nanopore Community Meeting 2021 about “Affordable GPU compute makes nanopore sequencing even more disruptive and empowering.”Benton is a senior scientist, bioinformatician, and an advocate of open, reproducible science. They share their materials on GitHub. Benton spoke about the birth […]
Jessica Blackburn from the University of Kentucky spoke at the Nanopore Community Meeting 2021 about “Detection of cell-free DNA in acute lymphoblastic leukemia patients to potentially identify CNS disease and monitor response to therapy.” Blackburn explained that acute lymphoblastic leukemia is the most common pediatric cancer, with ~3,000 children diagnosed each year. They explained that […]
Megan Radosevich from Carroll College presented at the Nanopore Community Meeting 2021 on “Analyzing regional and seasonal microbial community variation from a contaminated Montanana river.” Their project is called CREWS: Consortium for Research on Environmental Water Systems that is funded by the Montana NSF EPSCoR Partnership with several colleges and universities in Montana. A central […]
Miten Jain from the University of California, Santa Cruz presented at the Nanopore Community Meeting 2021 on “Nanopore sequencing updates using Q20+ and R10.4.” While this may not be the latest technology, I think it is useful to learn about the history and how improvement were made. Jain spoke about the early version of ultra-long […]
Alexander Wittenberg from KeyGene in the Netherlands presented at the Nanopore Community Meeting 2021 on “Accuracy improvements in crop genome assembly using the Q20+ chemistry.” They presented on improvements in sequencing and crop assembly using Q20+ chemistry. KeyGene is using genome assembly and the early access ONT program to identify pan-genome and variants. KeyGene has […]
Henri van Kruistum presented at the Nanopore Community Meeting 2021 on “Allele-specific DNA methylation in the live-bearing fish Poeciliopsis gracilis.” Kruistum is a Ph.D. student at Wageningen University in the Netherlands. They are working on the Poecillidae live-bearing fishes. There are sever species and on the genomic level there is interest in learning about the […]
Jae Young Choi from New York University spoke at the Nanopore Community Meeting 2021 about “Unlocking the plant 3D genome architecture with Pore-C sequencing.” They spoke about how the genome is folded in a 3D conformation in the nucleus. There have also been many techniques to understand the folding. One such technique is Pore-C sequencing: […]