Metagenomics

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Faster Turnaround in Infectious Disease Diagnosis with Metagenomics

Judith Breuer from the UCL Institute of Child Health in the UK presented at London Calling 2025 a session titled “How could we incorporate metagenomics into routine diagnostic microbiology?” Breuer defined metagenomics and explained how their work on rapid respiratory metagenomics. In the winter of 2024/2025, the group adapted their clinical metagenomics approaches for rapid […]
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Implementing Rapid Metagenomics Protocols in Healthcare

Tonight I returned from my first SABER East! It was a lot of fun! The video I watched tonight was Judith Brueur from the Great Ormond Street Hospital (GOSH) discuss the implementation of a respiratory metagenomics protocol at Guy’s and St. Thomas’ Hospital (GSTT) using Oxford Nanopore Technologies (ONT). The protocol was developed by the […]
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Exploring Metagenomic Tools: Kaiju, GOTTCHA2, and More

Tonight I continued watching the recording for the ISME19 workshop “From Reads to Function” corresponding to the last part of Day 1. Ben Allen from KBase described completeness and contamination of bins/MAGs. The next step in the workflow is taxonomic assessment and classification. First, one option is to classify taxonomy of metagenomic reads with Kaiju. […]
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Understanding Metagenomics Workflows in KBase

I continued watching the ISME19 Workshop “From Reads to Function” day 1 sessions. Next, Ben Allen from KBase spoke about “Metagenomics in KBase.” Allen went over metagenomics workflows in KBase. They explained that the workflow is based on the Chivian et al. (2023) Nature Protocols publication. Allen shared a graph with the NCBI Sequencing Read […]
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Metagenomics Explained: From DNA Reads to MAGs

Tonight I continued watching the ISME19 Workshop by KBase: “From Reads to Function, Day 1.” Kelly Wrighton presented on “Metagenomics 101: From Reads to Bins.” Wrighton is at Colorado State. Wrighton co-runs the Microbial Ecosystems Lab. They defined microbiome as “the study of microorganisms, their genomes, and their surrounding chemical and other environmental conditions.” I appreciate how this […]
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BugSeq’s Innovative Approaches to Virus Detection

Tonight I continued watching the ONT webinar on advances in genomic profiling of respiratory viral pathogens. The second speaker was Nick Gauthier from BugSeq. The title of their session was “Translating metagenomics to the clinic.” The BugSeq team is working to develop clinical metagenomic pathogen agnostic approaches. BugSeq started working on an ONT mNGS platform […]
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Rapid Viral Genome Sequencing: Highlights from a Recent Webinar

I watched the webinar tonight facilitated by Anna Maria Niewiadomska, Global Market Segment Manager in Public Health at Oxford Nanopore Technologies. They first spoke about using ONT for microbiology and infectious disease work. The turnaround time with the rapid library prep was one feature that Niewiadomska highlighted, as well as the real-time analysis and read-length […]
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Challenges in Clinical Sequencing Techniques

Tonight, I continued watching the Oxford Nanopore Technologies London Calling 2024 expert panel on “Building a rapid, targeted, and responsive infectious disease system.”Aaron Pomerantz, the Global Segment Marketing Associate Director at ONT, facilitated the session. All panelists were invited to the stage after doing brief introductions. Rahul Batra from Guy’s and St. Thomas’ NHS Foundation Trus […]
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Building Effective Multi-Disease Surveillance Systems

Tonight, I started watching the Oxford Nanopore Technologies London Calling 2024 expert panel on “Building a rapid, targeted, and responsive infectious disease system.”Aaron Pomerantz, the Associate Director of Global Segment Marketing at ONT, helped facilitate the session. Dr. Ines Hassan from the Tony Blair Institute for Global Change started. Hassan helps encourage the development and […]
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FDA’s Precision Genomics: Modernizing Food Safety Techniques

The Precision Genomics session at the Nanopore Community Meeting in Boston included a session by Julie Haendiges from the U.S. Food and Drug Administration. They explained that they are tasked with safeguarding more than $1.5 trillion worth of food, cosmetics, and dietary supplements. Haendiges spoke about how they are modernizing and optimizing methods. They explained […]
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