Month: October 2023

Checking MAGs

The next lesson in the Nanopore Learning Metagenomics course that I watched tonight was “Introduction to metagenomic assembly.” Tim Walker from the Technical Services Group at ONT introduced metagenomic assembly as reconstruction of reads into corresponding genomes. Metagenomic assembly is a computational process, said Walker, and the contigs may resemble the genomes or plasmids. Metagenome […]
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The Cloud-based EPI2ME Metagenomics Workflows

Tim Walker from the Technical Services Group conducted a demonstration of EPI2ME as part of the Nanopore Learning course. Walker noted that EPI2ME currently hosts free metagenomic classification pipelines including WIMP, the antimicrobial resistance workflow, and the Fastq 16S workflow. The 16S workflow works with the 16S barcoding kit. This is the kit and workflow […]
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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 […]
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MinKNOW Features and Run Assessment

Marta Verdugo from Oxford Nanopore Technologies is the presenter for the Nanopore Learning sessions I watched tonight. The series of videos focused on MinKNOW and setting up an experiment. Verdugo provided an overview of the MinKNOW graphical user environment. In the second video of the series, they set up a control experiment. One experiment setup […]
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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 […]
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ONT Library Preparation Options

Tonight I continued watching the Nanopore Learning sessions about Metagenomics. The Metagenomics lessons I started with were “Library Preparation: An introduction and overview of the options available.” Hazel Johnson provided an overview of the library preparation protocols and kits offered. They defined library preparation as “converting sample into format compatible with the sequencing system” by […]
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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 […]
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RNA Structural Detection and Pore-CUPINE

Yue Wan from the Genome Institute of Singapore presented at the Nanopore Community Meeting in Singapore on “Detecting RNA structures using nanopore sequencing.” Wan’s lab has been using Nanopore to study RNA structures. Traditionally, chemical probes were used to determine structure. However, short-read high-throughput structure probing is challenging because of long complex protocols and RNAs […]
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Training for m6A Identification

Jonathan Goke from the Genome Institute of Singapore presented at the Nanopore Community Meeting in Singapore on “Identification of m6A RNA modifications at single molecule resolution using nanopore direct RNA-seq data.” They are working on methods to analyze transcriptomes and are interested in the epitranscriptome. Goke explained that m6A is one of the most frequent […]
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