Softwares

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. […]
Read more

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 […]
Read more

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 […]
Read more

Nanocompore for Signal Comparison

Tommaso Leonardi from the Italian Institute of Technology (IIT) presented a lightning talk at London Calling 2019 on “signal level RNA modifications detection in eukaryotic non-coding RNAs.” Leonardi explained that there are many RNA modifications, and they developed the tool Nanocompore to compare signals from two conditions. It also takes into account replicates. Nanopore also […]
Read more

A Thirty-year Old SIV Sample

“Looking for a needle in a haystack: nanopore sequencing of a new Simian immunodeficiency virus (SIV) from a chacma baboon (Papio usrinus)” is the title of Susan Engelbrecht’s 2019 London Calling session. Engelbrecht, from Stellenbosch University in South Africa, spoke about primate lentiviruses and their “extreme genetic variability.” SIV is a retrovirus about 9 kb […]
Read more

Molecular Tagging with Unique DNA and Squiggles

Tonight, I watched a 2019 London Calling session by Katie Doroschak from the University of Washington on “Molecular tagging with nanopore-orthogonal DNA strands.” Molecular tagging systems use DNA to identify physical objects. Doroschak shared examples of secret exchange and counterfeit pharmaceutical detection. The research team used the MinION and created digital tags and codewords with […]
Read more

Unraveling Transcriptional Complexity with Direct RNA Sequencing

Daniel P. Depledge from New York University presented at London Calling 2019 on “Redefining the transcriptional complexity of viral pathogens using direct RNA sequencing.” Depledge started with a slide and the question: Got herpes? They are fascinated with herpes viruses and their multiple features and applications. Herpes simplex virus type 1 (HSV-1) is a 152 […]
Read more

Sequencing Australian Plant Viruses

Monica Kehoe from the Department of Primary Industries and Regional Development in Australia presented at the 2019 London Calling meeting. The session’s title was “Nanopore sequencing and analysis of plant pathogenic viruses—more than just rapid diagnostics?” Kehoe is based in Western Australia and using Nanopore sequencing to sequence RNA plant viruses. Their focus is to […]
Read more

nano-COP to Investigate Nascent RNA Splicing Dynamics

Heather Drexler from Harvard Medical School presented at London Calling 2019 on “Direct sequencing of nascent RNA exposes splicing kinetics and order.” For example, Drexler explained that RNA splicing is complex, with distant exons being joined. Drexler emphasized that transcription rates affect alternative splicing and that transcription and splicing are physically and mechanistically coupled. The […]
Read more

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 […]
Read more
Press ESC key to close search