Softwares

December 5, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

The Evolution of MinKNOW

The Knowledge Exchange video series had one on MinKNOW features and Updates that I watched tonight. MinKNOW has evolved in the past couple of years! Rich Roman, a Technical Product Manager from ONT, described the changes in Model Selection and incorporation of the Flip Flop Basecalling model. The high accuracy (HAC) basecalling model contains a […]

December 4, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Multiplexing and Demultiplexing

Tonight I watched the November 13, 2018 recording of the “Sample barcoding: Sequencing in multiplex and Demultiplexing” Knowledge Exchange session in the Nanopore Learning Lesson Library. Julia Eales, an Application Scientist with Oxford Nanopore Technologies and Philipp Rescheneder presented. Eales spoke about the uses of multiplexing. I didn’t know that with dual-barcoding you can multiplex […]

December 3, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

A Guide to Structural Variation Analysis

Today I watched the Knowledge Exchange session from Nanopore Learning about “A beginner’s guide to structural variation analysis: from discovery to basic annotation.” Steven Rudd, a bioinformatics expert at Oxford Nanopore Technologies, shared a couple of slides and then explored the structural variation tutorial. A structural variant (SV), Rudd said, is typically considered as “a […]

December 2, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Direct RNA Sequencing Explained

Tonight, I watched the Nanopore Learning Knowledge Exchange about Direct RNA Sequencing. Libby Snell and Botond Sipos explained how the kit and process work. Snell began by addressing the question: why use direct RNA sequencing. They explained that it is truly native RNA sequencing since the RNA strand is read directly in the Nanopore. There […]

November 30, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

The Features of the GridION

Since we have the GridION and want to learn more about how to use it, I watched the Knowledge Exchange session about the “GridION Mk1: delivering the ultimate flexibility in the lab.” Jon Pugh spoke emphasized that Nanopore sequencing has the benefits real-time, on demand, and bioinformatics rich data. Oxford Nanopore Technologies (ONT) has the […]

Monitoring and Maximizing Flow Cell Use

I started watching videos from the Nanopore Learning Lesson Library. The Knowledge Exchange video “Getting the most out of a flow cell” caught my attention. Connie O’Donnell was the host and was joined by Anne-Marie Wadsworth who discussed tips to maximize flow cell use. Wadsworth explained that all flow cells have a maximum run time […]

November 28, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Improving Genetic Testing through 1000 Genomes Project

Danny E. Miller from the University of Washington presented at the Nanopore Community Meeting in Singapore on “The 1000 Genomes Project Oxford Nanopore Sequencing Consortium: expanding our understanding of human genetic variation.” They started by comparing the medical history and testing performed on two patients. Miller shared a linear workflow for traditional genetic workup. Miller’s […]

November 27, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares, Why

Structural Variant Detection and Analysis

Continuing with the Nanopore Learning course on Human Genome Sequencing and Analysis, tonight I watched the video about structural variation detection. Anthony Doran, a member of the Technical Services Team with Oxford Nanopore Technologies, defined structural variation as large structural changes in your sample compared to the reference genome. The examples Doran shared on a […]

November 26, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

SNP and Indel Detection Tools

Tonight I watched the next video of the Human Genome Sequencing and Analysis course that is part of Nanopore Learning. The lesson is an “Introduction to SNP and Indel Detection,” and Anthony Doran, a Technical Services Scientist, from ONT discussed bioinformatics tools for SNP and indel detection. Doran spoke about the need to map/align reads […]

November 25, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Nextflow and EPI2ME Labs Workflows in a Terminal

I want to learn how to use EPI2ME and EPI2ME Labs effectively. The Nanopore Learning course has several videos about EPI2ME Labs. The one I watched tonight was about “EPI2ME Labs Nextflow Workflows demonstration” by Dilrini De Silva, a Technical Applications Scientists in Bioinformatics at Oxford Nanopore Technologies. In the video, De Silva demonstrated running […]

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