EPI2ME

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Enhanced Clinical Data Analysis with Integrated EPI2ME and MinKNOW

Tonight, I watched the London Calling 2024 session about EPI2ME workflows. The title was “Product demo: Integrated EPI2ME: streamlined analysis for clinical and biopharma applications.” Matt Parker from ONT is a clinical scientist. They spoke about AmPORE-TB, human variation workflows, and mRNA vaccine quality control. The tuberculosis workflow aims to rapidly identify antimicrobial resistance in […]
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EPI2ME Everywhere: New Workflows and Cloud Integration

We have been using EPI2ME a lot lately and want to learn more about the new features. Tonight, I watched Sirisha Hesketh, Clinical Bioinformatician from Oxford Nanopore Technologies, present “EPI2ME everywhere” at London Calling 2024. They began with an overview of the workflows available: seventeen ranging from base calling and alignment to single-cell genomics. An […]
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Real-Time Analysis Challenges and RT-Metagenomics Workflow Demo

Tonight, I watched the London Calling 2024 EPI2ME Product Demo. The session title is: “EPI2ME: democratising bioinformatics – from point-and-click analysis to custom integrations.” Sarah Griffiths, ONT Bioinformatics Workflow Developer, gave an overview of the EPI2ME workflows. The workflows use Nexflow and containers. At the time of recording, they had seventeen workflows. Griffiths noted that […]
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SamnSero Workflow: Real-time Bacterial Genome Analysis

Tonight, I watched the London Calling EPI2ME product demo: “EPI2ME: democratising bioinformatics—from point-and-click analysis to custom integrations.” Natalia Garcia, a Bioinformatics Workflow Developer with Oxford Nanopore Technologies, explained how workflows use Nextflow and Docker containers. Seventeen workflows were available at the time of the recording during London Calling. Workflows can be run via the command […]
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Portable Lab for Wastewater DNA Extraction

Tonight, I started watching sessions from London Calling 2024! Rea Kobialka from the Institute of Animal Hygiene and Veterinary Public Health in Germany presented a session entitled “Mobile lab for rapid detection of pathogens in wastewater in sub-Saharan Africa.” They emphasized the importance of surveillance. The research team developed a portable suitcase mobile lab. The […]
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User-friendly Computational Workflows

Tonight I watched the EPI2ME updates from Matt Parker, Associate Director of Clinical Bioinformatics at Oxford Nanopore Technologies. We will use EPI2ME next week as part of the Portable Genome Sequencing course, focusing on bacterial genome assembly and metagenomics. This Nanopore Community Meeting Houston update started with a high-energy EPI2ME video highlighting updates to compute […]
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Digesting and Sequencing Stromatolites

I spent the day at ECU at the QM Summit! It was a lot of fun! Tonight, I watched Nicole Wagner from Georgetown University present on “Evolutionary history of conical stromatolites.” This is the last video of the metagenomics playlist! Conical stromatolites can be used to study their formation and used to learn about microbial […]
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Student Sampling of Contaminated Water Systems

Megan Radosevich from Carroll College presented at the Nanopore Community Meeting 2021 about “Analyzing regional and seasonal microbial community variation from a contaminated Montana river.” Radosevich did work over the summer and during a course in Montana. The project is part of the Consortium for Research on Environmental Water Systems (CREWS). One of the main […]
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EPI2ME Analyses Anywhere

Matt Parker, the Associate Director for Clinical Bioinformatics at Oxford Nanopore Technologies, spoke at the Nanopore Community Meeting in Houston about updates to EPI2ME. The session started with a new video about EPI2ME, highlighting the intuitive interface, real-time data, and cloud or local analyses. Parker said you can take a MinION and laptop into the […]
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Streamlined Nanopore Sequencing

“Reveal more: bring streamlined nanopore sequencing into your lab” is the title of the Nanopore Community Meeting Houston session I watched tonight. Rachel Rubinstein, a Technical Product Manager, explained new developments to streamline nanopore sequencing. Rubinstein emphasized “end-to-end” processes. They began describing the range of the PromethION devices, from the P2 to the PromethION 48. […]
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