Softwares

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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The Remora Update

Marcus Stoiber, a Principle Algorithms Researcher with Oxford Nanopore Technologies, presented at the Nanopore Community Meeting 2022 the “Nanopore modified base update.” Stoiber explained Oxford Nanopore sequencing allows for powerful epigenetics research because it can “directly detect methylation with high reproducibility and low bias.” You can sequence native DNA and RNA to assess modification. The […]
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DART and VolTRAX

Danielle Wrenn from the Institute of Artic Biology at the University of Alaska Fairbanks presented at the Nanopore Community Meeting 2022 on “DART: a toolbox for the rapid detection of antibiotic resistance.” Wrenn acknowledged the 2022 Genomics Hackathon in January 2022. They used Nanopore and adaptive sampling. Wrenn explained that DART’s purpose is “the rapid […]
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SLOW5 for Indigenous Genomics

Andre Reis from the Garvan Institute of Medical Research in Australia presented at the Nanopore Community Meeting 2022 on “A long-read nanopore sequencing platform for Indigenous genomics.” Their efforts to increase efforts to increase representation of Indigenous people in Australia. Reis spoke about indigenous Australians and the lack of representation in current catalogues. Thus, there […]
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New Oxford Nanopore Technologies

I am now watching videos from the Oxford Nanopore Technologies (ONT) YouTube playlist that includes sessions from the NCM 2022. I want to learn more about what others are doing with Nanopore and how to use automation and pipelines more efficiently. The first session I watched tonight was on “End-to-End human genome nanopore sequencing and […]
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Alignments and Assemblies

We began working with the VolTRAX2 today. I’m excited to use it for library preps along with the Miroculus Miro. Tonight I watched the NCM 2022 Masterclass session by Matt Attreed on “How to generate and call variants.” Attreed is a technical applications scientist (bioinformatics) with Oxford Nanopore Technologies. They began by providing an introduction […]
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Basecalling for Modified Bases

The Oxford Nanopore Technologies (ONT) NCM 2022 masterclass I watched tonight was “How to basecall your data and detect methylation” with Jessica Anderson, a field application scientist with ONT. The recording is available. Anderson described how Nanopore sequencing works: as DNA/RNA strands pass through the pore, changes in current are detected. Anderson explained that basecalling […]
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Flongles and Several MinIONs and PromethIONs

Austin Compton is a Technical Applications Specialist at Oxford Nanopore Technologies and presented a masterclass at NCM 2022. We’ve used the MinION but I don’t know as much about the PromethION and Flongle. Compton shared a slide that indicated that the Flongle flow cells have 126 pores, MinION flow cells have 512, and PromethION flow […]
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A Collection of Library Prep Options for Nanopore

Yan Yang from the Oxford Nanopore Technologies Technical Services North America West Coast Team, presented the NCM 2022 Masterclass “How to select the right library preparation workflow for your experiment.” Yang explained how Nanopore DNA/RNA sequencing works as the nucleic acid is passed through a nanopore and electrical signals are interpreted into sequence data. Yang […]
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