Year: 2024

Nanopore Sequencing and Bacterial Genome Assembly

Mantas Sereika from Aalborg University in Germany presented at the Nanopore Community Meeting 2021 a session with a title that caught my attention tonight: “Nanopore R10.4 enables near-perfect bacterial genomes.” They spoke about Nanopore sequencing raw read accuracy improvements and issues with homopolymers. Insertions and deletions in homopolymer regions can be an issue causing frameshifts. […]
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Exploring Plant Biodiversity with the Flongle

I am starting to watch older Oxford Nanopore Technologies (ONT) videos to prepare background information for the course we are developing. Tonight, I watched a session by Rob Harbert from Stonehill College. The title of the presentation was “Monitoring plant biodiversity in aquatic eDNA with low-cost Oxford Nanopore Flongle sequencing.”They used the Flongle for metabarcoding. […]
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Sequencing Plasmids Encoding KPC-2

Today, I spent time with the KBase Ed group at UC Berkeley! The first day was full of tips and opportunities. As I prepare for the Portable Genome Sequencing course later this semester, I am trying to learn about using Oxford Nanopore Technologies (ONT) devices for sequencing plasmids, microbes, metagenomes, and transcriptomes. Tonight, I watched […]
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Sequencing Large Environmental Plasmids

Tonight, I was searching for videos for the course I am preparing to teach on portable genome sequencing technologies. I want to discuss the use of long-read sequencing for identifying and characterizing native plasmids. I found an older yet very relevant London Calling 2019 session. Severine Rangama from the University of Warwick presented a short […]
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A Richer Transcriptome with FLAIR2

Colette Felton from the University of California at Santa Cruz presented at the Nanopore Community Meeting in Houston about “Haplotypes, isoforms, and fusions: towards a richer cancer transcriptome.” The Felton read studies splicing, and long reads could be used to detect isoforms. The lab developed a tool called FLAIR2 to study differential splicing. Felton’s lab […]
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MethPhaser and Improved Haplotype Phasing of Human Genomes

“MetaPhaser: methylation-based haplotype phasing of human genomes” is the title of the NCM Houston session I watched tonight. Yilei Fu from Rice University was the presenter. They began sharing how long reads provide more information about structural variations (SV) and help with assembly and phasing. Fu explained an example of thiopurine methyltransferase (TMPT) and how […]
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Update on Modified Base Detection and Methylation in Nanopore

Marcus Stoiber, Principal Algorithms Researcher with Oxford Nanopore Technologies, presented an update on modified bases at the Nanopore Community Meeting in Houston. They began describing how modified bases are detected from nanopore sequencing data. Remora detects modified bases on top of base calling. This is an analogy to Remora latching on to bigger fish and […]
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