Metagenomics

Workflows for Metagenomics and Isolate Genomes with ONT

The London Calling Metagenomics and isolate genome sequencing product demo was a fourteen-minute recording I watched tonight. The session was hosted by Rachel Rubinstein, a Technical Product Manager, Software, for Oxford Nanopore Technologies (ONT). Rubinstein spoke about using ONT for bacterial and viral genome sequencing. The goal of the session was to share applications using […]
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EPI2ME Workflows for ONT Data Analyses

Dilrini De Silva is a Field Applications Scientist in Bioinformatics for the EMEAI Region with Oxford Nanopore Technologies. De Silva presented a Masterclass at London Calling 2023 entitled “How to take your data analysis further.” This Masterclass focused on typical downstream analysis for several applications including genome assembly, variants, methylation, transcriptomics, and metagenome analysis. De […]
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Suggested Approaches for High-quality DNA and RNA

Vania Costa, a Field Applications Scientist with Oxford Nanopore Technologies (ONT), led the Masterclass I watched tonight. This session was part of London Calling 2023 and entitled “How to extract high-quality DNA and RNA.” I have watched a couple of Masterclasses Costa has created. The objective of this session was for users to determine appropriate […]
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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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CanMAGs from Long-read Assemblies

Anna Cusco from Vetgenomics in Spain spoke at the 2021 Nanopore Community Meeting about “Long-read metagenomics and Hi-C proximity ligation to characterize a canine fecal microbiome.” They have been characterizing microbiomes using metagenomics and Hi-C. The (now) classical approach is amplicon sequencing; however, it allows for taxonomic classification but not everything can be detected. With […]
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Point-of-care Metagenomics with ONT

Tonight I watched Madjid Morsli from the Mediterranean Infection Foundation and & Aix-Marselle University in France present at London Calling 2022 on “Point-of-care, real-time, metagenomics-based pathogen genome detection of life-threatening community-acquired meningitis.” They spoke about infectious bacterial meningitis and how the genotype of the pathogen affects prognosis. Morsli noted that at least 200 pathogens have […]
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Considerations for High-quality DNA and RNA for Oxford Nanopore Sequencing

Tonight I started watching Oxford Nanopore Technologies NCM 2022 Masterclasses. The first recording I watched was by Vania Costa on “How to extract high-quality DNA and RNA.” They spoke about considerations for different fragment lengths. For example, you may want long and ultra-long DNA fragments for assembly. However, for cell-free DNA sequencing you are likely […]
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