News!

April 22, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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: […]

April 21, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

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 […]

April 20, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]

April 19, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Pharmacogenetics with ONT

Yusmiati Liau from the University of Otago in New Zealand spoke at London Calling 2019 about “Nanopore sequencing of the CYP2D6 pharmacogene.” Liau explained that pharmacogenetics is used to learn about genes that affect responses to drugs. There is a standard nomenclature for pharmacogenetics. The PHarmVar database was used as an example. The CY2PD6 gene […]

April 18, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections

Fragmented Transcripts in Old Seeds

We are looking into the possibility of sequencing the genomes of ancient beans and corn. The London Calling 2019 session by Margaret Fleming from Clemson University seemed appropriate for tonight. The title of the session was “Using full-length transcript sequencing to reveal the fate of mRNA in aging seeds.” Seeds are not rocks: they are […]

April 17, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]

April 16, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, Softwares

Mobile Malaria Sequencing

Tonight, I found the “Mobile Malaria Project” session from London Calling 2019. Jason Hendry from the University of Oxford in the UK presented their malaria work. Fifty percent of the population was at risk in 2017! In 2008, resistance to artemisinin was found in Cambodia. In 2014, resistance spread across Southeast Asia. Chloroquine was the […]

April 15, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]

April 14, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]

April 13, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

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 […]