November 2023 – Carlos C. Goller

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 […]

November 24, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Overview of EPI2ME Labs Workflows

The Nanopore Learning course on Human Genome Sequencing and Analysis had a short video introducing the EPI2ME Labs workflows. Anthony Doran, a Technical Applications Scientist in Bioinformatics at Oxford Nanopore Technologies, spoke about the bioinformatics workflows available in EPI2ME Labs. Workflows were defined as multistep pipelines that may include many software and files at different […]

November 23, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, Softwares

The EPI2ME Labs wf-human-variation Workflow

Happy Thanksgiving! Tonight I watched a second video on EPI2ME Labs that is part of the Human genome sequencing and analysis course offered by Nanopore Learning. This half-hour video presented by Bala Periaswamy from Oxford Nanopore spoke about EPI2ME Labs and how it can run workflows through the use of Docker and Nextflow. The wf-human-variation […]

November 22, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

EPI2ME Labs as a Learning Platform

Tonight I started an EPI2ME Metagenomics workflow to analyze our two 16S runs for the metagenomics class. I also watched the Nanopore Learning Human Genome Sequencing and Analysis course video on “Data Analysis: EPI2ME Labs Introduction.” Anthony Doran, a member of the Technical Services Team with Oxford Nanopore Technologies, described EPI2ME Labs as a “point-and-click” […]

November 21, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Epigenetics and DNA Methylation Detection with ONT

Continuing with the Human genome sequencing and analysis Nanopore Learning course, tonight I watched the video on “Methylation Detection: Sample to Answer Workflow Overview.” Dilrini De Silva from the Technical Services Team at Oxford Nanopore started by defining epigenetics as the study of gene activity caused by chemical modification of nucleic acids, both DNA and […]

Month: November 2023