Canu

Genomic Surveillance of Multi-Drug Resistant Organisms with Long-Read Sequencing

Today was the first day of our IPERT Summer Workshops! I also started watching London Calling 2024 videos available on the YouTube channel. I began with the session titled “Genomic surveillance of multidrug-resistant organisms based on long-read sequencing.” Fabian Landman works at the Centre for Infectious Disease Control in The Netherlands and the Dutch National […]
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RAGE-seq and CITE-seq

Martin Smith from the Garvan Institute of Medical Research in Australia was mentioned in the London Calling 2019 session I watched yesterday. Today, I watched the recording of the 2019 London Calling session that Smith did on “Leveraging long reads for high-throughput multiomic analyses of cellular diversity in human tumours.” Smith wasn’t able to travel, […]
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Sequencing Sharks

Saili Johri from San Diego State University presented at London Calling 2019 on “Unraveling shark secrets: sequencing genomes and microbiomes for research and conservation.” Johri explained how they are using the MinION to conserve sharks and rays. They emphasized how sharks are apex predators important for oceanic ecosystems and maintaining coral reefs. Sharks make direct […]
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Plant Genome Assembly Case Studies

Maximilian Schmidt from RWTH Aachen University in Germany presented at London Calling 2019 on “PLant de novo genome sequencing and assembly using Oxford Nanopore technology.” Schmidt spoke about extraction, sequencing, and bioinformatics as the three main phases of plant genome sequencing. They sequenced Solanum pennellii tomato. They incubated the plant in the dark for two […]
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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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Assembling Microbial Genomes from the Rumen

Amanda Warr from The Roslin Institute in the UK presented at London Calling 2019, “Going full circle: assembly of high-quality, single-contig microbial genomes from the rumen microbiome using long-read sequencing.” I had not watched this session before! They spoke about the rumen: a specialized stomach with a complex microbial environment. They are interested in the […]
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Developing Production Workflows for Long-read Data

Kiran V. Garimella from the Broad Institute spoke at the Nanopore Community Meeting 2019 about “Long-read genomes and transcriptomes on the cloud.” Garimella shared photos of the PromethION 48 at the Broad. They shared a graphic of the amount of data produced at the institute over the last decade. Garimella explained that at one point, […]
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Circularizing Genomes

Dylan Maghini from Stanford University presented at the Nanopore Community Meeting 2019 on “Genomes from metagenomes: assembling bacterial genomes with nanopore sequencing.” Maghini spoke about the importance of the human gut microbiome on human health. They noted that we still have an incomplete understanding of the gut microbiome. For example, de novo assembly aims to […]
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Characterization of Transgenic Constructs through Long-read Sequencing

Jolien D’aes from Sciensano, Belgium presented at the Nanopore Community Meeting 2021 on “Characterization of genetically modified microorganisms is facilitated by long-read whole-genome sequencing.” They explained that Sciensano is the Belgian science institute for food and animal safety. They monitor GMO-derived fermentation products. They may contain antimicrobial genes as resistance markers. Regulation prohibits the presence […]
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