genomics

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Sequencing Australian Plant Viruses

Monica Kehoe from the Department of Primary Industries and Regional Development in Australia presented at the 2019 London Calling meeting. The session’s title was “Nanopore sequencing and analysis of plant pathogenic viruses—more than just rapid diagnostics?” Kehoe is based in Western Australia and using Nanopore sequencing to sequence RNA plant viruses. Their focus is to […]
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User-friendly Computational Workflows

Tonight I watched the EPI2ME updates from Matt Parker, Associate Director of Clinical Bioinformatics at Oxford Nanopore Technologies. We will use EPI2ME next week as part of the Portable Genome Sequencing course, focusing on bacterial genome assembly and metagenomics. This Nanopore Community Meeting Houston update started with a high-energy EPI2ME video highlighting updates to compute […]
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Ultra-long Reads for Sea Snake, Lizard, and Dragon Genomes

I have been reading about the Ultra-long Sequencing Kit from Nanopore to try it this summer. Tonight I found the Ultra-long Reads YouTube playlist from ONT. I watched the session by Jillian Hammond from the Garvan Institute of Medical Research in Australia. They presented on the use of Ultra-long Reads for Australian Reptiles. They noted […]
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Spider Silk and Arachnid Genomes

Sarah Stellwagen from the University of Maryland, Baltimore County, spoke at the Nanopore Community Meeting 2019 on arachnids! The title of the session is “Advances in arachnid genomics using Oxford Nanopore’s MinION.” They study spider silk genetics and also harvestmen. Stellwagen explained that there are several different types of silk to make egg sacs, joints, […]
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Mitochondrial Genome Sequencing Reveals Variants

“Single-cell full-length nanopore sequencing for quantitative variant analysis of native and genome-edited mitochondria” is the title of the London Calling 2023 lightning talk I watched tonight. The presenter was Mo Li from King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. Li spoke about the human mitochondrial genome (mtDNA) and the challenges in […]
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Accuracy Improvements in Crop Genome Assembly

Tonight, I watched a recording from the Nanopore Community Meeting 2021 featuring Alexander Wittenberg from KeyGene in the Netherlands. They presented “Accuracy improvements in crop genome assembly using the Q20+ chemistry.” KeyGene is a crop innovation company, and they are generating new tools for genome assembly and structural variant analysis, among other analyses. They built […]
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Studying Centromere Structure with ONT

I continue to watch the YouTube “Assembly” playlist from the Oxford Nanopore Technologies (ONT) channel. Tonight, I watched session #8! Ian Henderson from the University of Cambridge in the UK presented at the Nanopore Community Meeting 2021. The session was titled “Assembling the centromeres – the ‘black holes’ of the genome.” Henderson said the centromeres […]
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Promoting Community and Biodiversity with Org.one

Tomas Marques-Bonet from the Institute of Evolutionary Biology in Spain spoke about the Org.one project at the Nanopore Community Meeting in 2021. The title of the session was “ORG.one: a new program to promote sequencing biodiversity.” They spoke about the mass extinction of species and the need to preserve biodiversity. Marques-Bonet explained how biodiversity genomics […]
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CanSeq150 to Sequence Canada’s Most Endangered Species

The London Calling 2021 session “CanSeq150: high-resolution genomic sequencing and assembly of 150 Canadian species” caught my attention today. Jahanshah Ashkani from Canada’s Michael Smith Genome Sciences Center was the speaker. The goal is to save Canada’s rich biodiversity by sequencing unique species. Loss of biodiversity is an issue: there are over 700 species at […]
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Genome-centric Metagenomics

Mads Albertsen, Associate Professor at Aalborg University, presented at the Nanopore Community Meeting 2017 on “Genome-centric metagenomics in the long-read era.” Albertsen talked about how we live in a bacterial world. However, only a small fraction can be grown. Single-cell genomics is challenging. Metagenomics has the potential to separate genomes through binning. Now you can […]
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