Softwares

Different Cytosine Methylations and DeepSignal-plant

Feng Luo from Clemson University presented at the Nanopore Community Meeting 2021 about “Genome-wide detection of cytosine methylations in plants from nanopore data using deep learning.” They are faculty in computer science at Clemson. They spoke about detecting methylation from nanopore signals. They developed the DeepSignal tool. Nanopore has developed Megalodon, and there is also […]
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Epigenetic Aging Clock for Cattle

Loan to Nguyen from The University of Queensland, Australia presented at the Nanopore Community Meeting 2021 on “An epigenetic aging clock for cattle using portable sequencing technology.” They spoke about the need learn birth date of cattle for breed registrations and genomic selection. However, there is no gene clock for cattle. Thus, they took sixty […]
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Genomic Technologies for STR Analysis

Ira Deveson from The Garvan Institute of Medical Research in Australia presented at the Nanopore Community Meeting 2021 on “Towards comprehensive genetic diagnosis of repeat expansion disorders with targeted nanopore sequencing.” Deveson spoke about the ReadUntil function also known as adaptive sampling to selectively sequence molecules. Short tandem repeats (STRs) are 2-12 bp sequence motifs […]
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Use of Oxford Nanopore Technologies for Microlab Development

Rajesh Pandey from the CSIR-Institute of Genomics and Integrative Biology in India presented at the Nanopore Community Meeting 2021 on “Genomic surveillance for future pandemic preparedness.” The lab does integrative genomics of host-pathogen interactions focusing on high-throughput and high-priority sequencing while trying to maintain cost efficiency. They have a sample to sequence microlab workflow using […]
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A Quail Genome with Methylated Repeats

Elena Bolshakova from Herzen State Pedagogical University of Russia presented at the Nanopore Community Meeting 2021 on “DNA methylation analysis of a tandem repeat specific to Coturnix japonica using nanopore sequencing.” They mentioned that tandem repeats are poorly understood and yet important for the regulation of gene expression and chromosomal structure. Nanopore sequencing allows methylation […]
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Long-read Sequencing Can Identify RNA Isoforms and NMD Modulators

Evangelos Karousis is a Senior Researcher at the University of Bern, Switzerland and presented at the Nanopore Community Meeting 2021 on “Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells.” They began by describing what nonsense-mediated mRNA decay (NMD) can do how how they can be dangerous. Endogenous mRNAs can be targeted by NMD. In […]
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AmplideX PCR and Nanopore Sequencing for Carrier Screening

Sarah Statt presented at the Nanopore Community Meeting 2021 on “AmplideX PCR and nanopore sequencing deepens analysis and simplifies workflows for carrier screening.” Statt is an R&D Senior Manager at Asurgen, a Bio-Techne Brand. They spoke about the technologies needed for carrier screening. The company created AmplideX that includes long-range PCR and long-read sequencing to […]
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Genome-wide Protein Interactions with DiMeLo-seq

Annie Maslan from the University of California, Berkley spoke about “Mapping protein-DNA interactions genome-wide with DiMeLo-seq as part of the Nanopore Community Meeting 2021. They explained that existing methods for mapping protein binding use coverage as a proxy for binding.” Maslan noted that short-read methods obscure or complicate the interpretation of joint and independent binding […]
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Near-perfect Bacterial Genomes and MAGs

Mantas Sereika, a Ph.D. student at Aalborg University in Denmark, spoke at the Nanopore Community Meeting 2021 about “Nanopore R10.4 enables near-perfect bacterial genomes.” This topic is of interest for several of the courses I teach. Sereika spoke about the improvements in accuracy of Nanopore sequencing. Raw read accuracy has increased but there are still […]
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