sequencing

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 25, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

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 […]

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 […]

October 23, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]

October 22, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]

October 21, 2023
By Carlos C. Goller
Diversity, Oxford Nanopore Technologies, Reflections, sequencing

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 […]

October 20, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares, Why

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 […]

October 19, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Population-level Detection of Structural Variants and their Features

Fritz Sedlazeck from Baylor COllege of Medicine & Rice University, presented at the Nanopore Community Meeting in Singapore on “Comprehensive structural and copy number variant detection: from mosaic to population-level.” Sedlazeck and their team have developed numerous tools for structural variation (SV) detection. SV, Sedlazeck noted, are fewer than SNP but have profound impacts. Long […]

October 18, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Consensus Somatic SV Calling Using Long Reads

Tonight I watched a session from the Nanopore Community Meeting in Singapore entitled “Investigating structural variations and complex cancer genomes using Oxford Nanopore sequencing” presented by Marjan Naeini from the Garvan Institute of Medical Research in Australia. Naeini described the primary classes of structural variations (SVs) as deletions, duplications, inversions, insertions, and translocations. They studied […]

October 17, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Nanopore Sequencing for Detection of Modifications in Cancer Genomics

Genta Nagae from the University of Tokyo in Japan presented at the Nanopore Community Meeting in Singapore on “Direct detection of DNA modifications in human cancer genomes.” Nagae briefly spoke about the significance of DNA methylation in biology and cancer. They used the QIAamp and Puregene kits from QIAGEN to prepare tumor DNA for sequencing […]