Oxford Nanopore Technologies

Oxford Nanopore Technologies Masterclass: DNA and RNA Extraction Recommendations

We start the Portable Genome Sequencing course tomorrow! I wanted to review the latest Oxford Nanopore Technologies (ONT) recommendations for extracting DNA and RNA. The London Calling 2024 session “How to extract high-quality DNA and RNA” was the one I watched tonight. Vania Costa, a Field Applications Scientist with ONT, presented this ONT Masterclass. This […]
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Nanopore Sequencing: Experiment Planning and Workflow Breakdown

As we prepare for the start of a new semester, I decided to watch a Masterclass from London Calling 2024. Akelia Wauchope-Odumbo, Associate Director Technical Applications—Americas with Oxford Nanopore Technologies, presented on experimental design. The session title was “How to get started with nanopore sequencing and plan your experiment.” The masterclass series guides users from “sample to […]
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Nanopore NO-MISS Workflow for Bacterial Genomes

We are going to use the Nanopore NO-MISS workflow. It will be used to sequence several microbial isolates. This is part of the Portable Genome Sequencing course. In preparation, this London Calling 2024 session seemed useful. Alex Trotter, Development Scientist, and Chris Alder, Bioinformatician, are both at Oxford Nanopore Technologies. They presented “How to sequence […]
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Shifting to Oxford Nanopore for Clinical 16S rRNA Gene Sequencing

Trish Simner is the Director of Bacteriology and Infectious Disease Sequencing Laboratories. They work at the Johns Hopkins University School of Medicine in Baltimore, Maryland. They presented at London Calling 2024. The session’s title was “Bringing Nanopore Sequencing into the Clinical Microbiology Setting with Targeted Approaches.” Simner spoke about the advantages of long reads and […]
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Ultra-fast Deep-learned CNS Tumor Classification using Nanopore-sequencing

I watched a session from the Oxford Nanopore Technologies Clinical & Biopharma Day tonight. It was held on May 24, 2024 (part of London Calling 2024). Professor Pieter Wesseling is from the Princess Maxima Center for Pediatric Oncology in the Netherlands. He is also from the Amsterdam University Medical Centers. He presented the session titled […]
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Improved Plant Genome Assembly with Ultra-Long Nanopore Sequencing

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 […]
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Ultra-Rapid, Long-Read Whole-Genome Sequencing with BadgerSeq

Stephen Meyn from the Center for Human Genomics and Precision Medicine at the University of Wisconsin-Madison presented at London Calling 2024. The session title was “BadgerSeq: a deecentralized model for ultra-rapid, long-read, whole-genome sequencing.” Meyn spoke about rare genetic disorders in the NICU and the importance of diagnosis. Meyn emphasized the need for speed and […]
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Long-Read Sequencing and Methylation Pattern Characterization in 1000 Genomes Project

Sophia Gibson from the University of Washington presented at London Calling 2024 on “Haplotype-resolved repeat expansions & methylation patterns in 1000 Genome Project data.” Gibson noted that clinical genetic testing typically requires multiple tests and clinic visits… and is diagnostic in fewer than 50% of cases. This is described as the “diagnostic odyssey.” Long-read sequencing […]
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KeyGene’s Innovative Approach to Banana Pangenome Research

Alexander Wittenberg from KeyGene in the Netherlands spoke at London Calling 2024 about “Unlocking the banana pangenome: harnessing genetic diversity.” They explained that the genetic diversity of bananas is very low because of the passaging of a single clone. Fusarium wilt and black Sigatoka cause disease and elicit the spraying of large amounts of pesticides. […]
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