Month: May 2023

Workflows and Tools for Assemblies and Variant Calling

Matt Attreed presented at the Nanopore Community Meeting 2022 on “How to generate assemblies and call variants.” This is a Masterclass and started by describing the resources on the Nanopore website. There is a page dedicated page on Nanopore accuracy information. The session included different workflows that process FASTQ files to SAM, BAM, and other […]
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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- and Ligation-based Sequencing of mtDNA

Andrea Legati from The Foundation of the Carlo BEsta Neurological Institute, IRCCS, Italy, spoke at the Nanopore Community Meeting 2021 on “Mitochondrial DNA analysis by long-read NGS in patients affected by mitochondrial diseases.” Legati spoke about the role of mitochondria in ATP production and metabolites and the significance of mitochondrial DNA (mtDNA) deletions. There are […]
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Midnight and ARTIC SARS-CoV-2 Protocol Comparisons

Julie Karl & Robert Maddox from the University of Wisconsin-Madison presented at the Nanopore Community Meeting 2021 about “SARS-CoV-2 sequencing: on the midnight train to throughput.” They started with statistics from November 11, 2021 about global COVID-19 cases, including data from GISAID. The GISAID graph showed which countries had contributed to the database. Karl shared […]
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Methplotlib and the Development of Tools for Allele-specific Methylation in the Human Brain

Wouter De Coster from the VIB Center for Molecular Neurology in Belgium presented a session for the Oxford Nanopore Community Meeting 2020 entitled “Allele-specific methylation in human brains.” De Coster is a bioinformatician and started with a quote from Sydney Brenner: “Progress in science depends on new techniques, new discoveries and new ideas, probably in […]
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Whole Plasmid Nanopore Sequencing

Tonight I watched the “Plasmid sequencing, assembly and analysis workflow” video with speaker Jon Pugh, Associate Director of Platform Marketing at Oxford Nanopore Technologies. The whole plasmid nanopore sequencing workflow allows for sequencing analysis of inserts, promoters, and backbones. With Nanopore sequencing, it is possible to use a single technique “in-house.” The workflow they suggest […]
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Detecting RNA Modifications with Nanocompore

Logan Mulroney from EMBL-EBI and IIT-CGS Italy presented at London Calling 2022 on “Detecting RNA modifications from nanopore ionic current signals.” They spoke about chemical and physical modifications of RNA and how they are “really dynamic.” I did not know there are “eraser” proteins that remove modifications, “writers” that add the modification, and “readers” that […]
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SNP Analyses for Gorilla Conservation

Ettore Fedele from the University of Leicester in the UK presented at London Calling 2022 on “Genomic tools for gorilla population dynamics and conservation.” Fedele spoke about using Oxford Nanopore Technologies (ONT) sequencing to support conservation of gorillas and began by emphasizing the importance of gorillas and major threats they encounter. Monitoring species to combat […]
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