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Innovations in Genetic Testing: The CRDC’s Impact

Wanqing Shao from Boston Children’s Hospital presented at the Nanopore Community Meeting on “Maximizing the power of genomic sequencing in pediatric rare disease.” Shao is a Genomics Scientist working in a collaborative team: the Children’s Rare Disease Collaborative (CRDC). They are interested in rare and complex diseases that are often misdiagnosed. Shao also noted that […]
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Liftoff and Novel Gene Annotation

Alaina Shumate from Johns Hopkins University was a speaker at the Nanopore Community Meeting 2021. Shumate was a graduate student and worked on “The annotation of novel genes in a complete human genome.” They noted that in 2003, scientists “finished” the human genome, but reions were still incomplete. In 2021, the Telomere-to-Telomere (T2T) Consortium was […]
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Starting to Assemble Genomes

Eoghan Harrington and David Stoddard from Oxford Nanopore Technologies presented on December 18, 2018 about Assembly as part of the Nanopore Learning Knowledge Exchange series. They are both in the Applications group. Harrington started by sharing how they approach new assembly projects from planning to sequencing. They listed the steps: planning, sequencing, assembly, and quality […]
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Identifying Methylation States with MinKNOW

Dilrini De Silva, a Technical Applications Scientist in Bioinformatics at Oxford Nanopore Technologies, spoke about Methylation Detection on MinKNOW as part of the Human genome sequencing and analysis Nanopore Learning course. They discussed approaches for detecting methylation states with Nanopore sequencing and the MinKNOW software. MinKNOW includes models for methylation detection and mapping of reads. […]
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EPI2ME Workflows for ONT Data Analyses

Dilrini De Silva is a Field Applications Scientist in Bioinformatics for the EMEAI Region with Oxford Nanopore Technologies. De Silva presented a Masterclass at London Calling 2023 entitled “How to take your data analysis further.” This Masterclass focused on typical downstream analysis for several applications including genome assembly, variants, methylation, transcriptomics, and metagenome analysis. De […]
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Retrotransposon Insertions in Rare Diseases

Belen de la Morena-Barrio from the University of Murcia, Spain presented at London Calling 2023 on “Nanopore sequencing reveals retrotransposon insertions or complex genetic mechanisms in four rare disorders.” Morena-Barrio spoke about the impact of “rare” diseases and the challenges of diagnosis. They noted that often it takes four or five years for accurate diagnosis […]
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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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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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