Year: 2024

Improving Blood Typing

Nicholas Gleadall from the University of Cambridge in the UK presented at London Calling 2019 on “Blood donor genotyping—how can long-range sequencing help?” Gleadall spoke about blood transfusions and why blood type matching is needed. Current blood typing is done by serology with antibodies and agglutination. However, reagents are unreliable or not available for all […]
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A Useful Genome Assembly Report

John Davey from the University of York in the UK presented at London Calling 2019 on “Tapestry: assessing small eukaryotic genome assemblies with long reads.” Davey spoke about the tool and mentioned they are a Nanopore Service Certified core. Davey spoke about Galdieria sulphuraria with a genome of 10-20 Mb with several chromosomes. This organism […]
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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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Repeat Expansion Analysis

Pay Giesselmann from the Max Planck Institute for Molecular Genetics in Germany presented at London Calling 2019 on “Nanopype: processing and quantification of short tandem repeats.” The team created a data processing pipeline for targeted repeat expansion analysis and worked on STRique to quantify repeat expansion. Nanopype can be installed from the source, used as […]
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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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Reporter Proteins for Protein Sequencing

Jeff Nivala from the University of Washington presented at London Calling 2019 on “Multiplex direct quantification of barcoded protein reporters on a MinION.” Nivala explained that they have been working on single-molecule protein sequencing with a nanopore… focusing on proteins! The team developed an “unfoldase” mechanism to translocate proteins through nanopores. Their goal is protein […]
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Identifying Full-length Transcripts through Innovative Capture Techniques

As part of the 2019 London Calling lightning talks, Silvia Carbonell Sala from the Centre for Genomic Regulation in Spain presented on “CapTrap-CLS: full-length RNA capture long-seq for GENCODE.” They explained how our genomes encode long non-coding RNAs. Their functions, however, may not be known. Carbonell Sala is part of the GENCODE lncRNA Capture Project […]
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