November 2023 – Page 2 – Carlos C. Goller

November 20, 2023
By Carlos C. Goller
Metacognition, Reflections, sequencing, Softwares

Data Analysis Solutions from ONT

The next lesson in the Nanopore Learning course for Human genome sequencing and analysis I watched was the introduction to data analysis solutions video. The speaker, Anthony Doran, shared a graphic with the different bioinformatics options provided by Oxford Nanopore. EPI2ME is the real-time cloud-based platform. There are several workflows for quality control, alignment, 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 […]

November 15, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Identifying Methylation States with MinKNOW

Dilrini De Silva, a Technical Applications Scientist in Bioinformatics at Oxford Nanopore Technologies, spoke about Methylation Detection on MinKNOW as part of the Human genome sequencing and analysis Nanopore Learning course. They discussed approaches for detecting methylation states with Nanopore sequencing and the MinKNOW software. MinKNOW includes models for methylation detection and mapping of reads. […]

November 14, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Setting up MinKNOW for Kit 14

Tonight I continued with the Human genome sequencing and analysis course from Nanopore Learning. I watched the video about MinKNOW Configuration for Kit 14. Bala Periaswamy from the Technical Applications Team spoke about setting up a MinKNOW run. They explained that kit 14 has improvements in the pore and motor enzyme. These changes result in […]

November 13, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Priming a Flow Cell and Setting up an Experiment in MinKNOW

Continuing with flow cell handling, the Human genome sequencing and analysis course from Nanopore Learning has a video entitled “A practical demonstration of priming and loading a flow cell.” In this short video, it is clear how the air pocket is removed with a P1000 set to 200 ul and slowly turned up to ~230. […]

November 12, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Handling ONT Flowcells

Every time I load another Oxford Nanopore Technologies (ONT) flow cell, I learn something new. Tonight, I watched the Nanopore Learning course on “Human genome sequencing and analysis” and the video about flow cell handling. Hazel Johnson, a Technical Services Specialist with ONT, explained the three flow cells available for ONT. The Flongle is designed […]

November 11, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

The MinKNOW Graphical User Interface (GUI)

Tonight I watched the MinKNOW GUI video from the Nanopore Learning course on Human Genome Sequencing and Analysis. Before watching these videos, I reviewed the Kit 14 videos. The MinKNOW graphical user interface (GUI) session was presented by Marta Verdugo from the Technical Services Team at Oxford Nanopore Technologies (ONT). The MinKNOW software is used […]

Month: November 2023