Year: 2024

The Mobile Suitcase Lab in Action

Tonight I watched the London Calling 2019 session by Ahmed Abd El Wahed from the University of Gottingen in Germany. The title of the presentation was “From ancient tomb to animal viruses: mobile suitcase lab for nanopore sequencing at field settings.” El Wahed spoke about the reagents and equipment needed to perform sequencing. They have […]
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Searching for Active Transposable Elements in Rice Genomes

Marie-Christine Carpentier, from the Genome and Plant Development Laboratory in France, presented at London Calling 2019 on “Using long-read nanopore sequencing to unravel structural variations in plants.” We have been trying plant genome sequencing and want to learn more. Carpentier spoke about transposable elements. Mobile elements can move within a genome. Carpentier noted that the […]
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Splicing Detection with Long Reads

Kuan-Ting Li from Cold Spring Harbor Laboratory presented at London Calling 2019 on “PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.” PSI-Sigma is a splicing detection tool that measures percent spliced in. With nanopore long-read RNA-seq data, PSI sigma presents a newer splicing detection approach. PSI-sigma was benchmarked on synthetic RNAs and […]
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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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