sequencing

Making Sense of Squiggles

James Ferguson from the Garvan Institute of Medical Research in Australia presented at London Calling 2019 on “SquiggleKit: a toolkit for manipulating nanopore signal data.” I had heard about the toolkit from another speaker and session. Ferguson spoke about the history of the toolkit and why they worked to develop SquiggleKit. They created five tools: […]
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Replication Fork Mapping in Eukaryotes

Magali Hennion from the Institute of Biology of the Ecole Normale Superieure in France presented at London Calling 2019 on “Mapping DNA replication using nanopore sequencing.” DNA replication in eukaryotes starts from multiple origins, and the fork progresses with variable speeds. Hennion explained that replication is important in understanding tumorigenesis. Single-molecule approaches are needed to […]
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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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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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