Softwares

At Home Mitogenomes

“Affordable de novo generation of fish mitogenomes using amplification-free targeted enrichment and deep sequencing of long fragments” is the title of the London Calling 2022 session by Ana Ramon-Laca from NOAA Fisheries and the University of Washington that I watched tonight. They began by talking about eDNA surveys and metabarcoding tools to survey environments. Ramon-Laca […]
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Sequencing to Safeguard the Kākāpō

Continuing with London Calling 2022 recordings, tonight I watched Marissa Le Lec from the University of Otago in New Zealand and Lara Urban from Helmholtz Munich, Germany speak about “Portable real-time sequencing to safeguard critically endangered wildlife.” They spoke about mammalian predators including domestic cats affecting bird diversity. Le Lec spoke about the kākāpō, a […]
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Ultra-rapid Nanopore Sequencing for Diagnosis

Tonight I watched John E. Gorzynski and Sneha D. Goenka from Stanford University present at London Calling 2022. Their fifteen-minute presentation entitled “Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing” was packed with information even though it was an informal session. This was an in-person session last year. Gorzynski is a postdoctoral scholar […]
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Differentially Methylated Regions and Acute Myeloid Leukemia

Alberto Magi from the University of Florence, Italy presented at London Calling 2022 a session called “Exploring the genomic and epigenomic landscape of acute myeloid leukemia with nanopore sequencing.” They spoke about the impact of acute myeloid leukemia and how they use patient samples to study this disease. They took three patient samples and timepoints […]
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Full-length Human mtDNA Sequencing with Cas9 Enrichment and ONT

Ibo Gut from CNAG-CRG in Spain presented at London Calling 2022 a session entitled “Novel method for multiplexed, full-length single-molecule sequencing of human mitochondrial DNA using Cas9-mediated enrichment.” I don’t know much about Cas9-mediated enrichment and have been curious. Gut spoke about mitochondrial DNA and how the human mitochondrial (mtDNA) is circular, 16.6 kb, has […]
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Real-time RNA Analysis with RISER

Adaptive sampling and real-time in silico enrichment have come up frequently in the last couple of months. I still haven’t used this feature and want to learn more. Tonight I watched the London Calling 2022 session by Alex Sneddon from the Australian National University entitled “RISER: real-time in silico enrichment of RNA species from nanopore […]
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Bacterial Race Typing with the Flongle

I was excited to come across an Oxford Nanopore Technologies YouTube video from London Calling 2022 that included the use of the Flongle! Abigail Stack from Bayer Crop Sciences spoke about “The POREtal to advancing plant diagnostics: Flongle for tomato bacterial race typing and beyond.” Stack started by explaining their role as a plant pathologist […]
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Mixing, Resequencing, and Deconvoluting

Alejandro Gener from the Association of Public Health Laboratories & Los Angeles County Public Health Laboratories, presented at London Calling 2022. Gener presented on “Assembly deconvolution resolves SARS-CoV-2 haplotypes in Delta-Omicron co-infections.” They described that between December 2021 and January 2022 Delta and Omicron strains of SARS-CoV-2 were circulating. Public health labs had to rule […]
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Early Detection of Changes in Esophageal Adenocarcinomas

Alvin Ng from the Early Cancer Institute at the University of Cambridge in the UK presented at London Calling 2022 on “Early detection of Barrett’s esophagus and esophageal adenocarcinoma using Oxford Nanopore long-read sequencing.” They began by explaining Barrett’s esophagus (BE) as the pre-malignant condition of esophageal adenocarcinoma (EAC) and has three stages: non-dysplastic, low-grade […]
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