Oxford Nanopore Technologies

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 […]

November 10, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

The Performance of Kit 14

The Nanopore Learning course on Human genome sequencing and analysis has a video on the Kit V14 performance. Vania Costa, a member of Oxford Nanopore Technologies Technical Services Team, explained how kit 14 uses R10.4.1 flow cells for increased simplex Q20+ accuracy and duplex Q30+ accuracy. The R9 kit will be discontinued at the end […]

November 9, 2023
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Oxford Nanopore Technologies Kit 14 Options

The Nanopore Learning course on “Human genome sequencing and analysis” has a video on Kit V14. Vania Costa, a Technical Services Specialist with Oxford Nanopore Technologies, described the accuracy of kit 14, which relies on R10.4.1 flow cells and pores. Costa explained that kit v14 has simplex Q20+ and duplex Q30+. Currently, there are ligation-based […]

November 8, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

The Versatile LSK

Continuing with the Nanopore Learning course on Human genome sequencing and analysis, tonight I watched the video with the title “Library preparation: Ligation sequencing kit.” Hazel Johnson, a member of the Technical Services Team with Oxford Nanopore Technologies, explained the basics of library preparation for Nanopore sequencing. They defined library preparation as “converting sample into […]

November 7, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Keeping the Pores Full

Improving sequencing yield is a goal we all have. Tonight I watched the video from the Nanopore Learning course on Human genome sequencing and analysis with the title “Improving sequencing yields: Getting the most out of your samples.” They noted the importance of keeping the flow cell pores full. For this, they recommend 5-50 fmol […]

November 6, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares, Transfer Students

Quality Control of Input DNA RNA

Continuing with the Human genome sequencing and analysis course, today I watched the video lesson on “Library preparation: Quality control of input DNA or RNA.” Hazel Johnson, a Technical Services Team member at Oxford Nanopore Technologies, explained that incorrectly quantifying DNA can result in reduced sequencing input. They do not recommend the use of NanoDrop […]

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