bioinformatics

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Duplications, Rearrangements, and Complex Bacterial Genomes

Tonight, I watched the London Calling 2019 session “Ultra-long reads and ultra-long duplications: deciphering the mysteries of the Bordetella pertussis genome.” Natalie Ring from the University of Bath in the UK was the presenter. They spoke about whooping cough and how the introduction of vaccination in the 1950s reduced the number of reported cases. In […]
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Eleven Human Genomes in Nine Days

Tonight, I watched Miten Jain’s London Calling 2019 presentation on “Generating high-quality reference human genomes using PromethION nanopore sequencing.” Jain is from the University of California, Santa Cruz. They have developed a framework to produce reference-quality human genomes in a week. Jain spoke about the need to sequence many human genomes that can serve 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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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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Liftoff and Novel Gene Annotation

Alaina Shumate from Johns Hopkins University was a speaker at the Nanopore Community Meeting 2021. Shumate was a graduate student and worked on “The annotation of novel genes in a complete human genome.” They noted that in 2003, scientists “finished” the human genome, but reions were still incomplete. In 2021, the Telomere-to-Telomere (T2T) Consortium was […]
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Developing Production Workflows for Long-read Data

Kiran V. Garimella from the Broad Institute spoke at the Nanopore Community Meeting 2019 about “Long-read genomes and transcriptomes on the cloud.” Garimella shared photos of the PromethION 48 at the Broad. They shared a graphic of the amount of data produced at the institute over the last decade. Garimella explained that at one point, […]
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Data Analysis Options with ONT

Tonight I watched the Nanopore Community Meeting Houston session by Bryant Catano, ONT Product Specialist. The session was a Masterclass entitled “How to get started with data analysis.” Catano spoke about the variety of options for data analysis available, from point-and-click to command line. Tools are available that are accessible, scalable, and versatile. Catano noted […]
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A Guide to Structural Variation Analysis

Today I watched the Knowledge Exchange session from Nanopore Learning about “A beginner’s guide to structural variation analysis: from discovery to basic annotation.” Steven Rudd, a bioinformatics expert at Oxford Nanopore Technologies, shared a couple of slides and then explored the structural variation tutorial. A structural variant (SV), Rudd said, is typically considered as “a […]
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Endangered Birds and Influenza

I continued watching London Calling 2023 Daily Preview recordings. Zoe McDougall spoke with Loic Lesobre and Stephanie Banakis. Banakis is from NIAID, NIH and Lesobre is from Reneco International Wildlife. Lesobre is involved in large scale breeding and conservation efforts, while Banakis works with influenza. They spoke about the overlaps in their work. Banakis discussed […]
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Clinicians and Bioinformaticians Using Nanopore for Diagnostics

Tonight I watched the London Calling 2023 panel “The future of clinical genomics.” Four panelists were asked several questions. The first was about the role of bioinformaticians in clinical work. One panelist spoke about how clinicians work on the automation and presenting the data. The exchange with bioinformaticians has helped the clinicians make the most […]
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