Oxford Nanopore Technologies

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 […]

November 19, 2023
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Sequencing Output and Data Analysis

I am on my way back from ASMCUE! It was a fun adventure. As I wait for my flight back to RDU, I was able to watch the Nanopore Learning course on Human genome sequencing and analysis and the video on “Introduction to data generation and sequencing output for analysis.” The presenter presented about the […]

November 18, 2023
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, sequencing

Real-time Analysis with EPI2ME

Tonight I watched another video from the Nanopore Learning course on Human Genome Sequencing and Analysis. This session was an introduction to real-time analysis. Sandra Guerra, a member of the Technical Services Specialist, introduced the tools for real-time data analysis. Guerra described the process of Nanopore DNA/RNA sequencing. They noted that Nanopore technologies and devices […]

November 17, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Assessing Runs with MinKNOW

I am at ASMCUE 2023 this weekend. Students set up a sequencing run without me and it is running. Tonight I watched the Nanopore Learning video from the Human genome sequencing and analysis course “MinKNOW: Assessing your run.” Marta Verdugo from the Technical Services Team with ONT described the flow cell health and percentage of […]

November 16, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Gbases and Basecallig

Continuing with the Human genome sequencing and analysis Nanopore Learning course, I watched the session entitled “MinKNOW: Live basecalling and output folder structure.” Marta Verdugo, a member of the Technical Services Team with Oxford Nanopore Technologies, introduced the different data types and how MinKNOW processes signals into reads. Each read corresponds to a signal from […]