Metagenomics

GROWdb Project: Sequencing Global River Ecosystems

Tonight I started watching the ISME19 Workshop by KBase: “From Reads to Function, Day 1.” Mikayla Borton was the first speaker of this session. The workshop had twenty-five people in person and ~220 virtual participants… from fifty countries. The KBase Education team was there! Borton’s session was on the Genome Resolved Open Watersheds database (GROWdb) […]
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Highlights from ENIGMA Workshop on Isolate Sequencing

Tonight I watched Lauren Lui from Lawrence Berkley National Laboratory present a “Long Read Isolate Sequencing and Assembly Workshop.” This session was recorded April 2, 2024 and was part of the ENIGMA program. Lui provided an overview of the apps they use: Filtlong, Unicycler, Polypolish, and Flye. The team was motivated by evolving long-read technologies […]
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Highlights from the Nanopore Biosurveillance Session

Tonight, I watched the recording of the Showcase Biosurveillance session at the Nanopore Community Meeting 2024. Ana Maria Niewiadomska, Segment Market Manager for Public Health with Oxford Nanopore Technologies, spoke to experts. Alex Kneubehl from Baylor College of Medicine spoke about his work on public health-related projects. Kneubehl and team have trained public health scientists […]
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Advancements in Nanopore Sequencing for Microbial Genomics

I continued watching the “Enhanced microbial profiling and metagenomics with nanopore sequencing” webinar. The second speaker was Steven Batinovic, a Field Application Scientist with Oxford Nanopore Technologies (ONT). The title of their session was “What you’re missing matters: delivering the future of microbial genomics with Oxford Nanopore.” Batinovic started by listing the microbiology and infectious […]
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Canine Microbiome Analysis at ASM Microbe 2024

The next talk in the session of Oxford Nanopore Technologies at ASM Microbe 2024. Anna Cusco, a postdoctoral researcher from Fudan University. Cusco spoke about pet health and dog microbiomes. Microbiome analysis can be performed with amplicons or whole genome information. They targeted full-length 16S sequencing to obtain genus and species-level information. One concern is […]
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Nanopore Sequencing Library Prep: Techniques and Comparison

Tonight, I watched Jessica Anderson, a Senior Field Applications Scientist with Oxford Nanopore Technologies (ONT), present at London Calling 2024. The session was part of the Masterclass 2024 series. It was titled “How to select the right library prep workflow for your experiment.” This session started with an introduction describing how nanopore sensing works. Anderson explained that during […]
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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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Genomic Studies of Adeno-Associated Virus Hepatitis: 2022 Pediatric Outbreak and Gene Therapy Effects

Oscar Enrique Torres Montaguth from the University College London in the UK presented a short talk at London Calling. The title was “Genomic studies of adeno-associated virus hepatitis.” They studied the 2022 pediatric hepatitis outbreak using metagenomic sequencing approaches. They identified AAV2 in liver and blood samples of almost all cases, and adenoviruses and herpesviruses […]
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Rapid Pathogen Detection in Wastewater: Mobile Lab Setup and Method

I’m back home! I watched the London Calling 2024 session “Mobile lab for rapid detection of pathogens in wastewater in sub-Saharan Africa” by Rea Kobialka from the Institute of Animal Hygiene and Veterinary Public Health in Germany. Kobialka demonstrated the setup of the mobile lab suitcase for wastewater analyses. The suitcase lab needs a mobile […]
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