Reflections

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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Population Genomics in Thailand and Australia

Tonight I watched the Population Genomics Showcase Stage from the Nanopore Community Meeting in Singapore 2023. Warren Bach, ONT Senior Strategic Account Manager in Australia, was the moderator. Hardip Patel spoke about Australia’s National Centre for Indigenous Genomics, and Manop Pithukaporn presented on Thailand were the speakers. Hardip Patel from The Australian National University presented […]
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Inactivation of X Chromosome

Tonight I watched Quentin Gouil from the Walter and Eliza Hall Institute of Medical Research in Australia speak at the Nanopore Community Meeting in Singapore about “Measuring skewed X inactivation by adaptive nanopore sequencing.” Gouil explained that there are ~2000 genes on the X chromosome, and males are more affected by X-linked diseases. They described […]
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