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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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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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Long-reads Tools in KBase

I ran out of Nanopore videos on their YouTube channel! So I started watching a KBase webinar on long-read tools. Benjamin Allen from KBase introduced the session. This webinar will help me prepare for BIT 295 and isolate sequencing next semester. Allen shared KBase resources including the YouTube channel webinar recordings and the LISA Workshop […]
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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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Optimizing Cell & Gene Therapies with Multi-Omic Sequencing

Heather Stark, the Global Segment Manager at Oxford Nanopore Technologies, introduced the webinar “Enhancing Cell and Gene Therapy Success with Multi-Omic Sequencing: The Oxford Nanopore Advantage.” Start covers biopharma and explained how nanopore sequencing works. They explained that there are several end-to-end workflows for synthetic biology, including plasmid, AAV, amplicon, and mRNA IVT sequencing. Clark […]
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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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