Metagenomics

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ONT Learning: Metagenomics Planning

Tonight I started watching the ONT Learning sessions about Metagenomics. Tim Walker introduced options for metagenomics using nanopore sequencing. They defined metagenomics as “the genomic analysis of multiple organisms obtained from a single mixed sample.” The assembly of complete genomes and plasmids from mixed samples was one of several applications listed. Environmental monitoring and antibiotic […]
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Porcine Respiratory Disease Diagnostics

Nick Vereecke from PathoSense BV in Belgium presented at London Calling 2023 on “Coninfection in endemic influenza A virus-infected herds using nanopore metagenomic sequencing of tracheobronchial swabs.” Vereecke spoke about the complexity of porcine respiratory diseases: there is a mix of coronaviruses and bacteria. For some of the microbes involved, there are no lab culture […]
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Squiggle Analysis for Living and Dead Microorganisms

Tonight, I watched Harika Urel from the Helmholtz AI Institute and Technical University of Munich present a five-minute talk at London Calling 2023. The intriguing title of the recording is “Squiggle analysis for metagenomics viability inference.” Urel is a Ph.D. student in Dr. Lara Urban’s lab. I have watched several talks by Urban in the […]
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EPI2ME Labs Metagenomics Workflows on the Cloud

Tonight I watched the London Calling 2023 product demo for “Analysing bacterial genomes – from species identification to AMR.” Stephen Rudd, Director of Bioinformatics Product at Oxford Nanopore Technologies (ONT), shared their work on EPI2ME labs products. They have been developing EPI2ME Labs workflows for several years. These are pre-installed workflows that can help solve […]
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Developments in ONT from LC2023

Tonight I watched the “Welcome back to London Calling 2023” session. Rosemary Sinclair Dokos, Senior VP of Product & Programme Management at Oxford Nanopore Technologies (ONT) was the presenter and began day two of London Calling 2023 by talking about the journey of ONT. Sinclair Dokos found several parallels between the London Underground construction and […]
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Metagenomic Analysis of Water from Brazilian Reservoirs and Ponds

I am still thinking about the Nanopore talk I watched yesterday. I now want to try using Flongle flow cells again! Tonight, I watched Douglas Mendel from the University of Sao Paulo, Brazil present at London Calling 2022. The session was only six minutes long and had the intriguing title: “Comparative metagenomics of natural and […]
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An Impactful Practical

Reindert Nijland from the Wageningen University in the Netherlands wanted to teach more students about Nanopore and long-read sequencing. Nijland presented at the 2022 London Calling conference a very short (three minute) session describing how they use “Nanopore sequencing for biodiversity assessment in an educational setting.” They developed an Advanced Molecular Ecology course to help […]
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The Open Source CZ ID Pipeline

Tonight I watched Katrina Kalantar present a ten-minute session at the Nanopore Community Meeting 2022 entitled “CZ ID: an open-source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.” Kalantar is a computational biologist at the Chan Zuckenberg Initiative (CZI). I did not know about this pipeline! CZI is open-source and enables simple […]
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Carlos… speaks… slowly?

I finally did it. I watched our recorded presentation for the 2020 Lily Conference today. I recorded it in November in a single Zoom session with Deb and didn’t look back. I’ve been watching one or two recorded sessions each night and admiring the beautiful slides and thoughtful interactions presenters incorporated. I wondered: how long […]
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