Carlos C. Goller

January 25, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Mock Community and BAMBI Studies

Matthew Clark from The Genome Analysis Center presented at the Nanopore Community Meeting 2016 a session with the title “MinION metagenomics: from mock communities to clinical samples.” They took a mock community with twenty equimolar genomes. They were impressed with the results: 98%+ aligned, and there were long alignments. At the time, the group used […]

January 24, 2024
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Metagenomics-based Infection Diagnostics

Justin O’Grady, Associate Professor in Medical Microbiology at the University of East Anglia, presented at the Nanopore Community Meeting 2017 on “Rapid metagenomic diagnosis of hospital acquired pneumonia.” They spoke about the “loss” of effective antibiotics because of rising resistance. O’Grady suggests using metagenomics-based infection diagnostics to use narrow-spectrum antibiotics. Nanopore sequencing is useful because […]

January 23, 2024
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

MinHash for Rapid Pathogen Identification

Brian Ondov from the National Biodefense Analysis and Countermeasures Centre (NBACC) spoke at the Nanopore Community Meeting 2015 on “Leveraging MinHash for rapid identification of nanopore data on mobile hardware.” Ondov explained how the portability of the MinION device can be paired with portable hardware. They noted that memory expansion on a small device can […]

January 22, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Genome-centric Metagenomics

Mads Albertsen, Associate Professor at Aalborg University, presented at the Nanopore Community Meeting 2017 on “Genome-centric metagenomics in the long-read era.” Albertsen talked about how we live in a bacterial world. However, only a small fraction can be grown. Single-cell genomics is challenging. Metagenomics has the potential to separate genomes through binning. Now you can […]

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 20, 2024
By Carlos C. Goller
Reflections, Softwares

Sequencing C. bovis in the Field

Lewis Stevens from Northwestern University presented at the Nanopore Community Meeting 2019 on “Reference genomes from the field: the genome of Caenorhabditis bovis.” Stevens spoke about nematodes and their importance as parasites! Nematodes are estimated to infect 1.5 billion people worldwide! Wow! C. elegans is, however, distantly related to the nematode parasites. C. bovis may […]

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. […]