Softwares

Which ONT library prep kit do I choose?

Akelia Wauchope-Odumbo, a Technical Services Manager – Americas with Oxford Nanopore Technologies (ONT), led a Masterclass at London Calling 2023. I watched the recording tonight, as the session title aligns with the course goals for the ONT-based lab I am designing: “How to get started with nanopore sequencing and plan your experiment.” The session started […]
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Sequencing Borg Genomes

Marie Charlotte Schoelmerich from the University of California, Berkley presented at London Calling 2023 about “Confirmation of borg extrachromosomal genomes: analysis of their methylation patterns, metabolism, and tandem repeats.” Schoelmerich is a postdoc in Jill Banfield’s lab and spoke about the key role of microorganisms in methane cycles. Methane emissions are driving climate change, and […]
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Rapid Tuberculosis Drug Resistance Profiling from Sputum

Tonight the London Calling 2023 session I watched was presented by Tiana Schwab from the Institute of Social and Preventative Medicine at the University of Bern in Switzerland. The title is “Tuberculosis drug resistance profiling from native sputum using nanopore targeted sequencing: a field application study.” Schwab is working on a Ph.D. and described the […]
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Identifying and Plotting Short Tandem Repeats with Pathological Implications

Hagar Mor-Shaked from the Hadassah Medical Organization & Faculty of Medicine at the Hebrew University of Jerusalem in Israel presented at London Calling 2023 on “Pathological short tandem repeats analysis by long-read sequencing in affected individuals.” They explained that pathological repeat expansions can be found in coding and non-coding regions, and a few dozen have […]
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Using the PromethION for Human Genomics

The London Calling 2023 “Human genomics – from targeted to whole-genome sequencing” showcase recording is fifteen minutes long and highlights applications. Rachel Rubinstein, a technical product manager at Oxford Nanopore Technologies (ONT) shared various applications from targeted and whole genome de novo assembly. They spoke about the PromethION line of sequencing which can produce up […]
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CNV and SV Detection

Luis Paulin from the Baylor College of Medicine presented at London Calling 2023 a short session entitled “The long and short of structural variants using Oxford Nanopore Sequencing.” Paulin described how genomic variation caused structural variants (SV) and copy number variants (CNV). Using long-read technology allows for access to difficult to sequence genomic regions, thus […]
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Improved DNA and RNA Sequencing with R10.4.1 and Duplex Reads

Miten Jain from Northeastern University presented at London Calling 2023 about “A complete analysis of human genomes and transcriptomes using nanopore sequencing.” They spoke about R10.4.1 ultralong DNA sequencing. Jain’s group has been using this sample prep and flow cells with N50s between 90-110 kb and throughput of >100 Gb per PromethION flow cell. The […]
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New and Annotated Medically-relevant Genes Expressed in the Frontal Cortex

Bernardo Aguzzoli Heberle from the University of Kentucky presented at London Calling 2023 on “Oxford Nanopore long-read RNA sequencing enables precise RNA isoform discovery and quantification in human brains.” They shared an example of how longer reads allow for better RNA isoform quantification and discovery. Aguzzoli Heberle also noted that Nanopore sequencing yields more uniquely […]
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