genetics

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Roadkill for Genome Assemblies and Convergent Evolution Research

“Genomics from roadkill: high quality mammalian genomes using hybrid assembly with MinION long reads” was the title of Frederic Delsuc’s London Calling 2019 session. Delsuc is from the French National Centre for Scientific Research in France. Their lab specializes in mammalian phylogenomics. The project is called The ConvergAnt Project, which is “an integrative approach to […]
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Forensic Profiling with Nanopore Sequencing

Rebecca Richards from the University of Auckland in New Zealand presented at London Calling 2019 on “Biological evidence of the future: the use of sequencing in forensic science.” They spoke about forensic DNA profiling by analyzing STRs and capillary gel electrophoresis. This analysis looks at the length of the repeats. However, there are limitations: no […]
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Extracting and Sequencing Ultra-High Molecular Weight DNA

Nadie Holmes from the University of Nottingham in the UK presented at London Calling 2019 on “Extracting megabase DNA.” They work with DeepSeq providing training and core sequencing support. Holmes worked on collaborative projects to optimize ultra-long sequencing. They shared data from a 1.3 megabase read. They use the protocol developed by Josh Quick to […]
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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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Creating a Workflow for Pathogen Variant Detection with ONT

David Greig from Public Health England presented a session in London Calling 2019 with the title “Comparison of single nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin producing.” They explained how they work on pathogen surveillance and focus on STEC: Shiga toxin-producing Escherichia coli. […]
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Identification of Mutations in Cell Lines

Yukata Suzuki from The University of Tokyo in Japan presented at London Calling 2019 on “Identification of a new class of local copy number aberrations in lung cancer genomes using PromethION.” I thought this was timely since today, in class, we started sequencing redbud samples using a PromethION flow cell. Suzuki spoke about starting PromethION […]
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Sequencing on the Farm

Charles C. Kayuki from the Tanzania Agricultural Research Institute in Mikocheni, Tanzania, presented at London Calling 2019 on “Portable DNA sequencing in remote East African farms.” They are using genomics to fight plant pathogens, focusing on cassava. Kayuki explained that it is an easy crop to grow and drought-resistant. It is susceptible to two important […]
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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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Dark and Camouflaged Genes

Mark T.W. Ebbert from the Mayo Clinic presented at London Calling 2019 on “Long-read sequencing technologies resolve most ‘dark’ and ‘camouflaged’ gene regions.”Dark and camouflaged regions? Ebbert explained that regions can be dark because there are no reads available (“dark by depth“) or dark by low sequence quality (“dark by MAPQ“). Ebbert explained that most […]
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