Month: January 2024

Assembling Redwoods, Giant Sequoia, and a Fungus

“Sequencing and assembling the mega-genomes of mega-trees: the giant sequoia and coast redwood genomes” is the title of the session Steven Salzberg from Johns Hopkins University presented. I was curious why this session was classified as “Metagenomics.” Salzberg works on several different organisms. The project’s first results were released in April 2019, describing the genome […]
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Developing Production Workflows for Long-read Data

Kiran V. Garimella from the Broad Institute spoke at the Nanopore Community Meeting 2019 about “Long-read genomes and transcriptomes on the cloud.” Garimella shared photos of the PromethION 48 at the Broad. They shared a graphic of the amount of data produced at the institute over the last decade. Garimella explained that at one point, […]
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Simcere Diagnostics of Difficult-to-ID Organisms

Weizhi Chen from Simcere Diagnostics presented a lightning talk at the Nanopore Community Meeting 2017 titled “Nanopore metagenomics sequencing for identification of both culture-positive and culture-negative pathogens.”Chen explained how they are using MinION and sequencing for infectious disease diagnostics. These labs are associated with labs in China. The first case report Chen shared was the […]
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Multiple Enzymes and Beads for Longer Metagenomic Reads

Joshua Quick from the University of Birmingham in the UK has developed several Nanopore protocols and tools. Tonight I watched Quick present at London Calling 2019 on “The ‘Three Peaks Challenge’ and developing extraction methods suitable for long-read, ultra-deep stool metagenomics on the PromethION. Quick spoke about how they are studying fecal microbiome transplants for […]
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Mobile Metagenomics with MARTi

Richard Leggett from Earlham Institute in the UK presented at London Calling 2021 on “Real-time metagenomics with MARTi.” MARTi stands for “Metagenomic Analysis in Real Time.” They developed this workflow for rapid diagnostics. Once they developed MARTi, Leggett and the team realized there are numerous applications for “in situ sequencing.” NanoOK has been available but […]
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Metagenomics from Orthopedic Device-related Infections

Teresa Street from the University of Oxford in the UK presented at the Nanopore Community Meeting 2019 on “Metagenomic nanopore sequencing for analysis of orthopedic device-related infection.” Street spoke about the impact of hip, knee, shoulder, elbow, and ankle replacements and the percentage of revisions due to the suspicion of infection. Further surgeries are often […]
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Mock Community and BAMBI Studies

Matthew Clark from The Genome Analysis Center presented at the Nanopore Community Meeting 2016 a session with the title “MinION metagenomics: from mock communities to clinical samples.” They took a mock community with twenty equimolar genomes. They were impressed with the results: 98%+ aligned, and there were long alignments. At the time, the group used […]
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Metagenomics-based Infection Diagnostics

Justin O’Grady, Associate Professor in Medical Microbiology at the University of East Anglia, presented at the Nanopore Community Meeting 2017 on “Rapid metagenomic diagnosis of hospital acquired pneumonia.” They spoke about the “loss” of effective antibiotics because of rising resistance. O’Grady suggests using metagenomics-based infection diagnostics to use narrow-spectrum antibiotics. Nanopore sequencing is useful because […]
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MinHash for Rapid Pathogen Identification

Brian Ondov from the National Biodefense Analysis and Countermeasures Centre (NBACC) spoke at the Nanopore Community Meeting 2015 on “Leveraging MinHash for rapid identification of nanopore data on mobile hardware.” Ondov explained how the portability of the MinION device can be paired with portable hardware. They noted that memory expansion on a small device can […]
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Genome-centric Metagenomics

Mads Albertsen, Associate Professor at Aalborg University, presented at the Nanopore Community Meeting 2017 on “Genome-centric metagenomics in the long-read era.” Albertsen talked about how we live in a bacterial world. However, only a small fraction can be grown. Single-cell genomics is challenging. Metagenomics has the potential to separate genomes through binning. Now you can […]
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