assembly

Efficient Genome Assembly with Hifiasm

Haoyu Cheng from Yale University spoke at London Calling 2025 on “Efficient telomere-to-telomere genome assembly with nanopore reads using hifiasm.”Cheng described the challenges of assembling a diploid human genome. In 2022, the first telomere-to-telomere (T2T) human genome was published. One current strategy is to use long-read data and phasing. There are computational challenges. Hifiasm is […]
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Advancements in Bacterial Genomic Surveillance

Dr. Gabriel E. Wagner from the Medical University of Graz presented on “Reliable whole-genome genotyping for bacterial surveillance using nanopore sequencing data” as part of the Oxford Nanopore Technologies (ONT) YouTube series. Wagner spoke about the importance of genomic surveillance for both known pathogens and surveillance of variants, including antimicrobial and vaccine resistance. This topic, […]
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Advancements in Nanopore Sequencing: Insights from PAG Workshop

Tonight I watched the PAG Industry Workshop Oxford Nanopore Technologies offered on January 14, 2025. In this session, Aaron Pomerantz presented updates along with Sean Mckenzie that improve assemblies. The title of the session is “New assemblers enable unprecedented de novo genome and metagenome contiguity and completeness…” The series of talks include amplicon to massive […]
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Exploring N50 and Genome Assembly Techniques in KBase

Tonight I continued watching the LISA workshop videos. Lauren Lui from Laurence Berkley National Lab explained the apps available on KBase for long-read only and hybrid assemblies. Using a KBase narrative, Lui shared a Spades short-read-only assembly with 30~ contigs. They described the N50 as a metric for comparing genome assemblies. To calculate N50, contigs […]
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Understanding Hybrid Assemblies in Genomics Research

Tonight I watched the introduction to day 3 of the LISA workshop. Lauren Liu from Lawrence Berkeley Nation Laboratory spoke about how genomics research can be limited by incomplete genomes. They noted that “genomes are hypotheses about what microbes are doing… but with environmental sequencing we often don’t have complete genomes.” Liu explained that assembly […]
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Highlights from ENIGMA Workshop on Isolate Sequencing

Tonight I watched Lauren Lui from Lawrence Berkley National Laboratory present a “Long Read Isolate Sequencing and Assembly Workshop.” This session was recorded April 2, 2024 and was part of the ENIGMA program. Lui provided an overview of the apps they use: Filtlong, Unicycler, Polypolish, and Flye. The team was motivated by evolving long-read technologies […]
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Conservation Through Genomics: Org.one’s Impact on Endangered Species

It was nice to have a break and good food for Thanksgiving! Tonight, I watched the ORG.one session from the Nanopore Community Meeting 2024 in Boston. The session’s title was “ORG.one—enabling endangered species to bounce back,” which I enjoyed. Dan Fordham, the Director of Strategic Management with ONT and EMEA, was the facilitator of the showcase. The Org.one […]
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Personalized Diagnostics Through Nanopore Technology Advances

Tasos Gogakos from Arena BioWorks and Massachusetts General Hospital spoke at the ONT Biopharma Day. The title of the session was “Nanopore sequencing at the intersection between the clinic and biotech.”Gogakos is a clinical pathologist who recently started at Arena BioWorks. Gogakos began by sharing two clinical cases. The patient had lung cancer and molecular […]
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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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Tonight, I continued watching the Oxford Nanopore Technologies session from ASM Microbe 2024. The title of the session was “Celebrating a decade of DNA discoveries: 10 years of the MinION in microbiology.”Before the second speaker, the live sequencing demo was shown on the screen. The team was sequencing a microbe and had the audience guess […]
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