genomics

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Understanding DRAM and Genome Analysis at ISME19

I continue watching the ISME19 KBase workshop: “From Reads to Function, Day 2.” Jared Ellenbogen presented next. They spoke about “DRAM and genome-resolved inference.” Ellenbogen spoke about analyzing the fifteen genomes studied during the workshop with DRAM. The outputs of DRAM were described: a heat map with every row corresponding to a different genome or […]
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Insights into dRep and DRAM Tools for MAGs

Tonight I started watching day 2 of the ISME19 workshop “From Reads to Function.” Mikayla Borton from Colorado State University presented on “DRAM and genome-resolved inference.” Borton started with dereplication of bins/MAGs. After that step, MAGs are annotated with DRAM. The tool used to dereplicate metagenome assembled genomes (MAGs) is dRep. Borton explained that 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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Masterclass on Nanopore Sequencing: Expert Planning Tips

Tonight I watched an updated session entitled “How to get started with nanopore sequencing and plan your experiment.” The speaker was Akelia Wauchope-Odumbo, Associate Director of Technical Applications – Americas with Oxford Nanopore Technologies (ONT). Wauchope-Odumbo started this new masterclass series. The theme is “from sample to answer” covering preparation, sequencing, and analysis. The masterclass […]
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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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Transforming Cancer Care with Nanopore Sequencing

I continued watching the “Nanopore Sequencing Ultra Rich Data for Cancer Research” webinar. It featured Sayonika Mohanta, the Market Segment Manager for Methylation with Oxford Nanopore Technologies (ONT). Mathilde Fiser from the Curie Institute presentation had the title “Transforming Cancer Care: Redefining Cancer Characterization and Predisposition Insights through Nanopore Sequencing.” Fiser explained that the identification of germline alterations […]
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Current Trends in Precision Oncology for 2024

Tonight, I started watching a new session from the London Calling 2024 Clinical & Biopharma Day. The expert panel’s title was “Precision oncology: driving better outcomes for patients, health systems, and populations.” Olivier Lucas, the Director of Oncology with Oxford Nanopore Technologies (ONT), moderated the discussion. Four speakers began the session with brief introductions. William […]
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