Month: June 2023

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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The Centromeres through Nanopore Sequencing

Ian Henderson from the University of Cambridge in the UK spoke at the Nanopore Community Meeting 2021 about “The genetic and epigenetic landscape of the Arabidopsis centromeres.” They referred to the centromeres as “the black holes of the genome” and explained the “centromere paradox” because of their conserved function and diverse structure. Henderson and team […]
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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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Different Cytosine Methylations and DeepSignal-plant

Feng Luo from Clemson University presented at the Nanopore Community Meeting 2021 about “Genome-wide detection of cytosine methylations in plants from nanopore data using deep learning.” They are faculty in computer science at Clemson. They spoke about detecting methylation from nanopore signals. They developed the DeepSignal tool. Nanopore has developed Megalodon, and there is also […]
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Epigenetic Aging Clock for Cattle

Loan to Nguyen from The University of Queensland, Australia presented at the Nanopore Community Meeting 2021 on “An epigenetic aging clock for cattle using portable sequencing technology.” They spoke about the need learn birth date of cattle for breed registrations and genomic selection. However, there is no gene clock for cattle. Thus, they took sixty […]
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Genomic Technologies for STR Analysis

Ira Deveson from The Garvan Institute of Medical Research in Australia presented at the Nanopore Community Meeting 2021 on “Towards comprehensive genetic diagnosis of repeat expansion disorders with targeted nanopore sequencing.” Deveson spoke about the ReadUntil function also known as adaptive sampling to selectively sequence molecules. Short tandem repeats (STRs) are 2-12 bp sequence motifs […]
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