Oxford Nanopore Technologies

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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Afterwork Genome Sequencing and CRISPRoff

Sung won Lim from Binomica Labs in the USA did a flash talk at the Nanopore Community Meeting in 2022 about “MinION outcome in amateur research: three genomes from 2018 to 2022.” They started using MinION for fun as a “weekend project.” They sequenced Deinococcus radiophilus GCF 020889623.1 and compared it to other genomes deposited […]
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Influenza WGS Surveillance and Direct RNA Sequencing of Brain Samples!

Tonight I watched two short Nanopore Community Meeting 2022 recordings. I started with Sarah Scott from the the Minnesota Public Health Laboratory, USA who presented on the “Exploration of Oxford Nanopore long-read sequencing to contribute to influenza surveillance at the state level.” Scott is an APHL and CDC Fellow. Scott explained that genomic surveillance of […]
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NAb-seq to Confirm Antibodies

Kathleen Zeglinski from the Walter and Eliza Hall Institute of Medical Research in Australia presented the ten minute recorded session entitled “NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells” at the Nanopore Community Meeting 2022. Zeglinski explained that hybridomas and B cells are common […]
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Stereo Duplex Nanopore Sequencing

Katherine Lawrence, a Machine Learning Bioinformatician with Oxford Nanopore, spoke at the Nanopore Community Meeting 222 about “Advances in duplex basecalling.” They defined duplex sequencing as both ends of the DNA with adaptor motor proteins and two reads from the same molecule. Duplex basecalling incorporates information from both reads’ signals and improves accuracy with the […]
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The Mortino Genome

Karla Estefania Rojas Lopez presented at the Nanopore Community Meeting 2022 a ten-minute session entitled “Draft genome of mortino (Vaccinium florib), a wild berry species of the Andean paramo.” Rojas Lopez works at the Universidad de San Francisco de Quito in Ecuador. This is the second session I watch presented by a researcher from this […]
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Cell Line Sequencing and HPV Research

Isabel Rodriguez from the National Cancer Institute, USA spoke at the Nanopore Community Meeting 2022 on “Analysis of viral and human oncogene expression in human papillomavirus-driven cancer.” Rodriguez shared that human pipillomavirus (HPV) is responsible for almost all cervical cancer cases, the fourth most common cancer worldwide. I also didn’t realize that the incidence is […]
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