Oxford Nanopore Technologies

MAXQDA 101: A Beginner’s Guide to Qualitative Analysis

Alexis Chavez spoke at MAXDAYS 2025 on “MAXQDA 101: Essentials for new users.” Chavez is a graduate student at the University of Nebraska. Chavez explained that MAXQDA is capable of qualitative and mixed method analyses. The software also has tools for statistical analyses. Chavez noted that a general workflow within MAXQDA starts with organizing the […]
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Plant Genome Assembly Insights from ONT Workshop

Tonight I watched the Oxford Nanopore Technologies (ONT) PAG Industry Workshop session titled “A single-platform solution for plant de novo genome assembly.” Jeannie Mounger, a field applications scientist with ONT, was the presenter. They noted that for plant genome assembly there are several considerations. Plant genome size varies greatly: from Mb to Gb. Polyploidy varies […]
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Exploring Biodiversity with Oxford Nanopore Technologies and Barcoded Library Pools

Tonight I continued watching the PAG Industry Workshop offered by Oxford Nanopore Technologies. Sean Prosser from the University of Guelph presented “From pandemic preparedness to planetary biodiversity: ONT enables targeted amplicon sequencing at massive scale.” Prosser noted that there are almost 35,000 amplicon-based genetic tests available in the US per year. Prosser also noted that […]
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Genomic Surveillance of H5N1 in Dairy Products

Tonight I watched another PAG Industry Workshop session by Oxford Nanopore Technologies. This one was titled “Pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza in the United States.” Andrew Lail from the University of Wisconsin-Madison was the presenter. Lail explained that influenza is an RNA virus with 8 RNA segments. H5N1 influenza is […]
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Uncovering DNA Methylation to Save Sea Turtles

Why not end the day with The Turtle Project! Tonight I watched a session from the Oxford Nanopore Technologies (ONT) channel titled “The Turtle Project: Conservation epigenomics of endangered sea turtles with temperature-dependent sex determination.” Eugenie ‘Charley’ Yen from the Queen Mary University of London was the presenter. They started with a slide animation of […]
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Advancements in Nanopore Sequencing: Insights from PAG Workshop

Tonight I watched the PAG Industry Workshop Oxford Nanopore Technologies offered on January 14, 2025. In this session, Aaron Pomerantz presented updates along with Sean Mckenzie that improve assemblies. The title of the session is “New assemblers enable unprecedented de novo genome and metagenome contiguity and completeness…” The series of talks include amplicon to massive […]
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Exploring Microbial Genomics and Lanthanide Mining

Continuing with the LISA workshop, tonight I watched another session. This one was by a postdoc, Andrew Wilson, at Pacific Northwest National Laboratory. They have been working on plasmid and microbe sequencing. The title of the session was “Leveraging Long Reads for Synthetic Biology.” Wilson and team are using Gibson assembly and synthetic biology techniques. […]
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Key Insights from LISA Workshop on KBase Narratives

Tonight, I started watching the recording from day 3 of the LISA workshop. This session focused on the narrative for long-read assemblies. John-Marc Chandonia and Lauren Lui, Lawrence Berkeley National Laboratory explained the components of a KBase narrative. Chandonia demonstrated the apps panel, beta and released apps, and finding apps. The configuration of the Filtlong […]
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Understanding Hybrid Assemblies in Genomics Research

Tonight I watched the introduction to day 3 of the LISA workshop. Lauren Liu from Lawrence Berkeley Nation Laboratory spoke about how genomics research can be limited by incomplete genomes. They noted that “genomes are hypotheses about what microbes are doing… but with environmental sequencing we often don’t have complete genomes.” Liu explained that assembly […]
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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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