Softwares

Mapping Heterogeneity in DNA Replicaiton

“Untangling heterogeneity in DNA replication with nanopore sequencing” was the title of the London Calling 2019 session that Michael Boemo from the University of Oxford in the UK presented. Boemo spoke about how genome replication has been studied on average and not individual cases. DNA replication can be studied with next-generation sequencing methods to identify […]
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eDNA Monitoring and Jellyfish

Cheryl L. Ames from the US Naval Research Laboratory presented at London Calling 2019 on “Field-forward sequencing with Oxford Nanopore technology – a strategy to establish the upside-down mangrove jellyfish Cassiopea xamachana as a bioindicator.” They emphasized the biodiversity of the ocean is largely unexplored… and also threatened by climate change and overfishing. Environmental DNA […]
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Fungi and Dog Skin

I started watching London Calling 2019 sessions to learn about fungal genomics and assembly. Sara D’Andreano from the Autonomous University of Barcelona in Spain gave a “lightning talk” on “MinION application: performing long-fragment analysis on pure fungal cultures (3.5 kb and 6 kb) and genome analysis of Malassezia pachydermatis.” D’Andreano is a Ph.D. student working […]
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The Applications of the Suitcase Lab

Tonight I watched a London Calling 2023 session by Ahmed Abd El Wahed from Leipzig University in Germany. The title of the session is “Pathogen and species identification using a mobile suitcase laboratory,” which aligns nicely with the course I am teaching: Portable Genome Sequencing (PGS). The recording had videos outside highlighting the suitcase lab. […]
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Reticulatus

Samuel Nicholls from the University of Birmingham in the UK presented at London Calling on “Long-read nanopore metagenomics for reconstruction of bacterial genomes.” They spoke about the impact of microbial communities on human health and the difficulties we encounter trying to culture some microbes. Nicholls and team published a study sequencing the Zymo mock communities. […]
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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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Primer Pools and Phylogeographic Analyses

Today we started sequencing in the Portable Genome Sequencing course! We used several Flongle flow cells on the MinION run. I watched the session by Kame A. Galan-Huerta from the Autonomous University of Nuevo Leon, Mexico, tonight. They presented at the Nanopore Community Meeting 2022 on “Identification of resistance mutations to direct-acting antiviral agents against […]
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Microbial Bioprospecting in the Desert

Adriel Latorre-Perez from the Darwin Bioprospecting Excellence S.L. in Spain presented at the Nanopore Community Meeting 2021. I had watched this session previously and wanted to review it since I assigned a video this week related to bioprospecting. The title of the session is “A round trip to the desert: in situ nanopore sequencing informs […]
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Characterization of Genetically-modified Microorganisms

Jolien E’aes from Sciensano in Belgium presented at the Nanopore Community Meeting 2021. The title of the presentation is “Characterization of genetically modified microorganisms is facilitated by long-read whole-genome sequencing.” I don’t think I have watched this session before! D’aes explained how Sciensano, the Belgian Institute for Public and Animal Health. They focus on food […]
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