Softwares

Advancements in Structural Variant Detection with Sniffles2

Fritz Sedlazeck from Baylor College of Medicine spoke at the Nanopore Community Meeting in Boston on the “Detection of mosaic and somatic structural variants with Sniffles2.”Sedlazeck spoke about the advantages of long-read sequencing for structural variant detection. Their team is improving Sniffles2 for insertions and deletions and larger structural variants. Full structural variant genotyping requires […]
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Understanding Long-Read Phasing Methods in Genomics

Nikhita Damaraju from the University of Washington in Seattle presented at the Nanopore Community Meeting in Boston. The session’s title was “Evaluating the quality of long-read phasing methods in clinically relevant genes.” They explained that variants are inherited in equal measure. Damaraju defined phasing as the process of assigning variants to parental copies. Understanding which […]
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Revolutionizing Genetic Research: needLR Tool Explained

J. (Gus) Gustafson from the University of Washington spoke at the Nanopore Community Meeting in Boston about “needLR: a structural variant filtering and prioritization tool for long-read sequencing data.” They noted that half of suspected Mendelian conditions remain undiagnosed after current clinical testing methods. The Miller Lab at the University of Washington uses Oxford Nanopore […]
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Resolving DMD Intragenic Duplications with Nanopore Technology

Tonight, I watched Qiliang (Andy) Ding from the Mayo Clinic present at the Nanopore Community Meeting in Boston. The session’s title was “Resolving structural configurations of DMD intragenic duplications through nanopore long-read sequencing.” Ding is a Laboratory Genomics Fellow. Ding noted that the DMD gene encodes dystrophin, an essential protein for muscle function. This gene is associated […]
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Unlocking Plant Genetics: Insights on DNA Methylation in Maize

Jack Colicchio from Sound Agriculture in the US presented at the Nanopore Community Meeting in Boston on “DNA methylation patterns explain missing heritability in maize.” This ten-minute session was part of a breakout group. Colicchio spoke about the need for more resilient crops to address pollution, climate change, and population changes. They spoke about how, […]
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Ecuador’s Endangered Species: The Role of Genomics

Gabriela Pozo from the University of San Francisco de Quito in Ecuador presented at the Nanopore Community Meeting in Boston. The session’s title was “Obtaining reference genomes of emblematic and endangered Ecuadorian species.” Pozo noted that Ecuador is one of the seventeen megadiverse countries globally. However, conservation efforts are also needed. Genomics, noted Pozo, can […]
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Mapping Active rRNA Gene Clusters in Arabidopsis

Tonight, I watched a shorter Nanopore Community Meeting Boston session. Anastasia McKinlay from Indiana University & HHMI presented on “Positional mapping of active versus silenced rRNA gene clusters within A. thaliana nucleolus organizer regions. McKinlay spoke about nucleolus organizer regions in Arabidopsis thaliana. These positions are difficult to understand with shorter reads. Long-read sequencing helped […]
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Latest EPI2ME Features for Variant Analysis Explained

Matt Parker, the Director of Clinical Bioinformatics Software at Oxford Nanopore Technologies, facilitated the Nanopore Community Meeting Boston 2024 session on variant analysis with EPI2ME. The title of the presentation was “Ultra-rich human data – variant analysis with EPI2ME.” They shared the EPI2ME user interface updates that were recently released. There is a new element […]
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Exploring Single-Cell Sequencing with Oxford Nanopore

Tonight, I went into the lab to wash flow cells and try to reload the cDNA sequencing run. I may have caused more damaged… so I came back and watched the session “Individual cells matter – single-cell answers through nanopore sequencing.” Rachel Rubinstein, a Technical Product Manager at ONT, facilitated this showcase session. Rubinstein spoke […]
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Understanding the NO-MISS Workflow for Microbial Sequencing

Tonight, I watched the second half of a new Knowledge Exchange session focusing on “Sequencing and analysis of nanopore-only microbial isolates with the NO-MISS workflow.” Different extraction methods produced varying yields. Bead-beating and enzymatic lysis extractions affect read length and throughput, while fungal samples produce lower yields. Some potential issues include incomplete lysis and contaminants. Additional clean-up […]
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