Month: January 2024

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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EPI2ME Analyses Anywhere

Matt Parker, the Associate Director for Clinical Bioinformatics at Oxford Nanopore Technologies, spoke at the Nanopore Community Meeting in Houston about updates to EPI2ME. The session started with a new video about EPI2ME, highlighting the intuitive interface, real-time data, and cloud or local analyses. Parker said you can take a MinION and laptop into the […]
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2023 Dorado Updates

Joyjit Daw, a Principal Machine Learning Engineer at Oxford Nanopore Technologies (ONT), provided a Dorado update at the Nanopore Community Meeting Houston meeting. The Dorado v0.5.0 release supports core Guppy features, custom barcodes, read splitting, and Minimap2 alignment. Dorado has been integrated into MinKNOW. They have also extended features such as hemi methylation for the […]
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Dog Patients, Osteosarcoma, and Severus Structural Variant Analyses

Mikhail Kolmogorov from the National Cancer Institute, NIH, spoke at the Nanopore Community Meeting Houston about “Nanopore sequencing reveals structural heterogeneity in canine osteosarcoma.” Structural variants are any alterations greater than 50 bp. These events can affect one or multiple genes… or whole chromosomes! NCI has a comparative osteosarcoma (OS) program that recruits dogs nationwide. […]
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Streamlined Nanopore Sequencing

“Reveal more: bring streamlined nanopore sequencing into your lab” is the title of the Nanopore Community Meeting Houston session I watched tonight. Rachel Rubinstein, a Technical Product Manager, explained new developments to streamline nanopore sequencing. Rubinstein emphasized “end-to-end” processes. They began describing the range of the PromethION devices, from the P2 to the PromethION 48. […]
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Carrier Analyses using ONT

Bradley Hall from Asuragen presented at the Nanopore Community Meeting in Houston. The session was titled “AmplideX PCR and nanopore sequencing for accessible carrier screening for any lab.” Hall started by stating that “everyone is a genetic carrier of a disease or condition.” There are >2000 conditions, and carrier screening is often challenging for some […]
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