Year: 2023

Pore-C Reveals the Chromosomal Structure of Microbial Attachment

“Use of Pore-C to explore the 3D organization of animal symbiont chromosomes” was the title of the session Tobias Viehboeck from the University of Vienna, Austria, presented at the Nanopore Community Meeting 2022. They mentioned that there are approximately 1025 microbes that live associated with plants or animals. However, Viehboeck noted that few obligate symbionts […]
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Optimizing Wildlife Population Monitoring with ONT

Tonight I watched Jhakelin Gloria Reyes Vasquez from the Amazon Conservation Association in Peru present at the Nanopore Community Meeting 2022. The title of the fifteen-minute session was “Population monitoring with in situ conservation genetics in the Peruvian Amazon.” Reyes Vasquez spoke about the concept of one health that combines communication, collaboration, coordination and capacity […]
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Rapid Leukemia Subtype Classification with Nanopore

Melanie Sagniez from the CHU Sainte-Justine Research Centre in Canada presented on “Rapid leukemia classification using nanopore sequencing” as part of the Nanopore Community Meeting 2022. This ten-minute session described part of their Ph.D. project research. They first spoke about pediatric leukemia and the current diagnostic process. I didn’t realize that the process takes on […]
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The Open Source CZ ID Pipeline

Tonight I watched Katrina Kalantar present a ten-minute session at the Nanopore Community Meeting 2022 entitled “CZ ID: an open-source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.” Kalantar is a computational biologist at the Chan Zuckenberg Initiative (CZI). I did not know about this pipeline! CZI is open-source and enables simple […]
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Detection and Sequencing of Coronaviruses in Wastewater

Samuel Fisch from Tulane University School of Public Health and Tropical Medicine presented at the nanopore Community Meeting 2022 a ten-minute session on “Monitoring the circulation of SARS-CoV-2 variants through community wastewater sequencing.” Fisch stated that he goal was to “perform genomic sequencing on wastewater samples to detect variant changes within the local environment.” Wastewater […]
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Cattery Epidemiology

Nick Vereecke from PathoSense BV in Belgium presented “Intra- and inter-cattery epidemiology of feline coronavirus in Belgium between 2018 and 2021” as part of the Nanopore Community Meeting 2022. This five-minute session was packed with information. They described the feline coronavirus (FCoV) that was first detected in 1963 and has 3 serotypes so far. The […]
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The Serratia that Wasn’t Red… and Wasn’t marcescens

Levin Joe Klages from CeBiTec in Bielefeld University, Germany presented at the Nanopore Community Meeting 2022 on “Analysis of clinical research samples by nanopore sequencing with Q20+ chemistry reveals inaccurate classifications within the genus Serratia.” We used Q20+ chemistry to sequence a “red” isolate which ended up being Serratia according to our classification. I was […]
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Plasmids and Gene Transfers

Dr. Erin L. Young from the Utah Public Health Laboratory spoke a the Nanopore Community Meeting 2022. The ten-minute session was entitled “Long-read sequencing enables in-depth characterization of plasmids encoding KPC-2 in Citrobacter freundii outbreak. Young is a senior bioinformatician. Young explained that antimicrobial resistant (AMR) infections can be expensive and challenging to treat. Citrobacter […]
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Nanopore Sequencing Identifies Cable Bacteria

Mantas Sereika from Aalborg University in Denmark presented at the nanopore Community Meeting 2022 on “Targeted deep metagenomics for the recovery of novel closed microbial genomes from highly complex communities.” I thought this ten-minute session had an intriguing title, as I begin to wonder what we will do next in the BIT 295 course in […]
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Dorado is Here!

The Dorado basecaller has been on my mind and appearing in different Nanopore resources. Tonight I watched Mike Vella, Director of Machine Learning Operations at Oxford Nanopore Technologies, present an update on Dorado at the Nanopore Community Meeting 2022. Vella spoke about why we need another basecaller, as Nanopore has Bonito and Guppy. Vella explained […]
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