Softwares

Signal Analysis with Uncalled4

Sam Kovaka, a PhD candidate from Johns Hopkins University, spoke at the Nanopore Community Meeting 2021 about “Visualization and analysis of nanopore RNA and DNA signal alignments with UNCALLED4.” They explained adaptive sampling (AKA “ReadUntil“): “software-based targeted sequencing via selective ejection of reads” Kovaka explained that this requires rapid identification based on the beginning of […]
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Bioprospecting in the Spanish Desert

Adriel Latorre-Perez from Darwin Bioprospecting Excellence S.L. in Spain presented at the Nanopore Community Meeting 2021 about “A round trip to the desert: in situ nanopore sequencing informs targeted bioprospecting.” They defined microbial bioprospecting as “the search for biotechnologically-relevant products from microbial communities.” The products could be enzymes, molecules, or microbiomes. The process starts with […]
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Characterization of Transgenic Constructs through Long-read Sequencing

Jolien D’aes from Sciensano, Belgium presented at the Nanopore Community Meeting 2021 on “Characterization of genetically modified microorganisms is facilitated by long-read whole-genome sequencing.” They explained that Sciensano is the Belgian science institute for food and animal safety. They monitor GMO-derived fermentation products. They may contain antimicrobial genes as resistance markers. Regulation prohibits the presence […]
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Liftoff Annotation of Novel Genes from T2T Human Genome

Alaina Shumate from John Hopkins University presented at the Nanopore Community Meeting 2021 about “The annotation of novel genes in a complete human genome.” They began by describing how in 2003 scientists “finished” the Human genome Project but there still was missing sequence! In 2021, the Telomere-to-Telomere (T2T) Consortium actually completed the sequence of a […]
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Rapid Dog Infection Diagnosis

Natalie Ring from The Roslin Institute in the UK presented at London Calling 2022 on “DoGsTAils: developing nanopore-based diagnostic approaches for the effective antimicrobial stewardship of canine infections.” Ring spoke about skin and urinary tract infections in dogs and how they can be antibiotic resistant. It also often takes two days to obtain results. Thus, […]
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Improving ‘Noisy’ Long-read RNA-Seq

Chenchen Zhu from Stanford University presented at London Calling 2022 on the “Systematic assessment of long-read RNA-Seq datasets and its application in transcriptome analysis.” They are interested in understanding RNA isoforms using long-read sequencing. Differences in start sites and isoforms can lead to disease. The experimental workflow that Zhu shared was using reverse transcription and […]
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Fecal Samples for Epigenetic Age Estimations

Continuing with epigenetics, tonight I watched the London Calling 2022 session by Eveliina Hanski from the University of Oxford in the UK. The title of the session is “From laboratory to the wild: a non-invasive, MinION-based method for determining the epigenetic age of mice.” Hanski is a final year graduate student and is interested in […]
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The Epitranscriptome?

Eduardo Eyras from the Australian National University in Australia presented at London Calling 2022 a session entitled “RNA methylation detection at single-molecule resolution uncovers isoform-specific modifications during mouse brain development.” Eyras explained that chemical modifications of mRNA were discovered relatively recently and Boccaletto et al. 2021 noted >150 potential RNA modifications! However, only 6 have […]
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Screening for Klinefelter Syndrome

Anne Kristine Schack from the University of Copenhagen and gMendel, Denmark spoke at London Calling 2022 about “A novel assay based on Oxford Nanopore technology for potential mass screening of Klinefelter syndrome.” They explained that Klinefelter Syndrome is a genetic disorder in which there is an additional X chromosome and it affects one in 500 […]
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