Oxford Nanopore Technologies

January 21, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Characterizing Active Blueberry Microbiomes

Seda Mirzoyan from Rutgers University presented at the Nanopore Community Meeting 2019 on “Using SIP and MinION sequencing to uncover active microbial communities in blueberry farm and forest soil systems.” Mirzoyan characterized active communities by using SIP and the MinION system. They spoke about the United States being the largest blueberry producer, with over fourteen […]

January 19, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

The Challenges in Genome Assembly

Ryan Wick from the University of Melbourne spoke at the Nanopore Community Meeting 2017. They explained that assemblies still fail. The title of the session is “Assembly is still hard: challenges in genome assembly in the era of long reads.” Wick shared an example of a bacterial genome sequence that leads to inaccuracy in sequencing. […]

January 18, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, Softwares

Circularizing Genomes

Dylan Maghini from Stanford University presented at the Nanopore Community Meeting 2019 on “Genomes from metagenomes: assembling bacterial genomes with nanopore sequencing.” Maghini spoke about the importance of the human gut microbiome on human health. They noted that we still have an incomplete understanding of the gut microbiome. For example, de novo assembly aims to […]

January 17, 2024
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing

Rich Activated Sludge Communities

Caitlin Singleton from Aalborg University in Denmark presented at the Nanopore Community Meeting 2020 a session on metagenomic analyses titled “From MAGs to riches: exploring the microbial community of activated sludge using 1,083 high-quality metagenome-assembled genomes.” Singleton is a postdoc and explained why activated sludge is important. Activated sludge is used to treat wastewater to […]

January 16, 2024
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, Softwares

Nanopore Sequencing and Bacterial Genome Assembly

Mantas Sereika from Aalborg University in Germany presented at the Nanopore Community Meeting 2021 a session with a title that caught my attention tonight: “Nanopore R10.4 enables near-perfect bacterial genomes.” They spoke about Nanopore sequencing raw read accuracy improvements and issues with homopolymers. Insertions and deletions in homopolymer regions can be an issue causing frameshifts. […]

January 15, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Retrospective STEC Studies

This afternoon, I came back from visiting KBase in Berkeley. I am still watching sessions from previous London Callings to learn about different topics I will discuss in the upcoming Portable Genome Sequencing course. Tonight, I found the session by David R. Greig from Public Health England in the UK. Their 2021 London Calling session […]

January 13, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Sequencing Plasmids Encoding KPC-2

Today, I spent time with the KBase Ed group at UC Berkeley! The first day was full of tips and opportunities. As I prepare for the Portable Genome Sequencing course later this semester, I am trying to learn about using Oxford Nanopore Technologies (ONT) devices for sequencing plasmids, microbes, metagenomes, and transcriptomes. Tonight, I watched […]

January 11, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, sequencing, Softwares

A Richer Transcriptome with FLAIR2

Colette Felton from the University of California at Santa Cruz presented at the Nanopore Community Meeting in Houston about “Haplotypes, isoforms, and fusions: towards a richer cancer transcriptome.” The Felton read studies splicing, and long reads could be used to detect isoforms. The lab developed a tool called FLAIR2 to study differential splicing. Felton’s lab […]

January 10, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, Softwares

STRs and ONT for Forensic DNA Profiles

Rupesh Kesharwani from the Baylor College of Medicine, HGSC & University of North Texas HSC, presented at the Nanopore Community Meeting Houston on “STRspy 2.0: unlocking the potential of long reads for forensic DNA profiles.” They shared that STRs are short tandem 2-7 bp repeats that account for 3% of the human genome. Individuals have […]

January 9, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

MethPhaser and Improved Haplotype Phasing of Human Genomes

“MetaPhaser: methylation-based haplotype phasing of human genomes” is the title of the NCM Houston session I watched tonight. Yilei Fu from Rice University was the presenter. They began sharing how long reads provide more information about structural variations (SV) and help with assembly and phasing. Fu explained an example of thiopurine methyltransferase (TMPT) and how […]