Softwares

The Genomics England Long-read Sequencing Program

I am at the Gordon Research Conference in Maine. This is my first GRC! I was able to rest a little this afternoon and watched the London Calling 2023 session entitled “Genomics England long-read cancer whole -genome sequencing pilot” presented by Helen Webb from Genomics England, UK. Genomics England is also called GEL. Webb disclosed […]
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Deconvoluting Methylomes with Nanomix

Tonight I started watching videos from London Calling 2023! I started with the presentation by Jonathan Broadbent from the Ontario Institute for Cancer Research & the University of Toronto, Canada. Broadbent presented about “Nanomix: methylation-based cell-type deconvolution for low-pass nanopore sequencing.” They defined cell-free DNA (cfDNA) as “a mix of DNA from blood cells and […]
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Direct RNA Sequencing Identifies NMD Targets

Anna Glushkevich from the Shmyakin-Ovchinnikov Institute of Bioorganic Chemistry in the Russian Federation, presented at the Nanopore Community Meeting 2021 on “Direct RNA sequencing reveals unusual NMD targets in plants.” They study nonsense-mediated RNA decay (NMD), a mechanism that regulates up to 10% of cellular transcripts! This is the second time I hear about Nanopore […]
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Profiling Gene Expression of Pediatric Leukemia Samples

Jeremy Wang from the University of North Carolina at Chapel Hill presented at the Nanopore Community Meeting 2021 on “Classification of pediatric acute leukemia using full-length transcriptomics.” This research was a collaboration for a pediatric oncologist also at UNC. They spoke about the variation in treatment of pediatric cancers based on local. Cellular and genetic […]
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CanMAGs from Long-read Assemblies

Anna Cusco from Vetgenomics in Spain spoke at the 2021 Nanopore Community Meeting about “Long-read metagenomics and Hi-C proximity ligation to characterize a canine fecal microbiome.” They have been characterizing microbiomes using metagenomics and Hi-C. The (now) classical approach is amplicon sequencing; however, it allows for taxonomic classification but not everything can be detected. With […]
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Barcode-aware Sequencing

Alexander Payne from the University of Nottingham in the UK presented at the 2021 Nanopore Community Meeting about “Barcode-specific adaptive sampling – from human gene panels to viral amplicons.” They spoke about ReadFish or “Read Until” which is an adaptive sampling toolkit. They ran an experiment with four different species to test adaptive sampling for […]
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Remora Brings the Mods

Marcus Stoiber, a Senior Data Analyst at Oxford Nanopore Technologies (ONT), presented on “Nanopore methylation: a better way to mods” at the Nanopore Community Meeting 2021. Stoiber and team devised the Remora modified base detection framework. Remora separates methylation/modified base calling from the basecalling neural networks. This separation provides high accuracy for methylation calls and […]
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Detection of Pathogens from Aerosols at Wastewater Treatment Facilities

High E. Olsen from the University of California, Santa Cruz presented at the Nanopore Community Meeting 2021 on “Detecting SARS-CoV-2 and other pathogens in aerosols at wastewater treatment plants.” The title is really intriguing! Wastewater, Olsen said, is a catalog of human pathogens and also a source of aerosols because of the aerators used. The […]
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Capacity Building and Surveillance in Senegal

Abdou Padane from the Institute for Health Research, Epidemiological Surveillance and Training (IRESSSEF) in Senegal, spoke at the Nanopore Community MEeting 2021 about the “Molecular distribution of SARS-CoV-2 in Senegal.” Padane is a medical researcher, doctoral student, and manager for the BSL3 lab! They noted that Senegal is a West African country with free movement […]
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ecDNA Sequencing and Assembly

Tonight, the IPERT summer workshops ended. Sissel Juul & Phill James presented at the Nanopore Community Meeting 2021 about “For want of a nail: investigating somatic and germline variations in cancer.” They are both at Oxford Nanopore Technologies in the Genomics Application Team. In 2021, they spoke about extrachromosomal DNA in cancer. Juul spoke about […]
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