ONT

March 2, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections

Squiggle Analyses for Dead or Alive Inference

Harika Urel, a Ph.D. student in Lara Urban’s lab at the Helmholtz Al Institute and Technical University of Munich in Germany, presented at London Calling 2023 on “Squiggle analysis for metagenomic viability inference.” I watched this session a couple of months ago and wanted to return to it in preparation for summer research and the […]

January 11, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, sequencing, Softwares

A Richer Transcriptome with FLAIR2

Colette Felton from the University of California at Santa Cruz presented at the Nanopore Community Meeting in Houston about “Haplotypes, isoforms, and fusions: towards a richer cancer transcriptome.” The Felton read studies splicing, and long reads could be used to detect isoforms. The lab developed a tool called FLAIR2 to study differential splicing. Felton’s lab […]

January 3, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Streamlined Nanopore Sequencing

“Reveal more: bring streamlined nanopore sequencing into your lab” is the title of the Nanopore Community Meeting Houston session I watched tonight. Rachel Rubinstein, a Technical Product Manager, explained new developments to streamline nanopore sequencing. Rubinstein emphasized “end-to-end” processes. They began describing the range of the PromethION devices, from the P2 to the PromethION 48. […]

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

Coverage, Binning, and Dereplication of Metagenomic Data

The last session of the Oxford Nanopore Technologies Nanopore Learning Metagenomics course is about additional metagenomic concepts. Tim Walker spoke about metagenomic assembly: “the computational process which seeks to reconstruct the microbial genomes within a metagenomic mixture.”The assembled reads could be genomes or plasmids. Metagenomic assembled genomes (MAGs) can be used for several analyses. Coverage […]

October 29, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Metagenomic Classification and ONT Reads

Tim Walker from the Technical Services Team with Oxford Nanopore Technologies presented the Nanopore Learning Course – Metagenomics lesson I watched tonight. They spoke about metagenomic classification techniques to identify organisms from sequence data and annotate genes. For targeted metagenomics, ITS, 16S, or antibiotic resistance genes can be amplified and sequenced. Whole genome sequencing can […]

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

PCR-based ONT Kits and 16S Analysis

Tonight I continued watching the Nanopore Learning Metagenomics series. The lessons focused on Library Preparation: Low input PCR kits. Hazel Johnson spoke about low-input kits. Library preparation involves attachment of sequencing adapters that are “Y” shaped and include a motor protein and leader sequence. A tether site facilitates the capture of the molecule. When you […]

October 24, 2023
By Carlos C. Goller
Online Learning, Reflections, sequencing, Softwares

ONT Learning: Metagenomics Planning

Tonight I started watching the ONT Learning sessions about Metagenomics. Tim Walker introduced options for metagenomics using nanopore sequencing. They defined metagenomics as “the genomic analysis of multiple organisms obtained from a single mixed sample.” The assembly of complete genomes and plasmids from mixed samples was one of several applications listed. Environmental monitoring and antibiotic […]