genetics

February 23, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, Softwares

Mitochondrial Genome Sequencing Reveals Variants

“Single-cell full-length nanopore sequencing for quantitative variant analysis of native and genome-edited mitochondria” is the title of the London Calling 2023 lightning talk I watched tonight. The presenter was Mo Li from King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. Li spoke about the human mitochondrial genome (mtDNA) and the challenges in […]

February 20, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Structural Variants from the Bovine Long Read Consortium

I am continuing to watch the London Calling 2023 on-demand lightning talks. Tonight, I watched the session “Discovering the missing variation: a long-read sequencing study into the structural variation in two dairy breeds” by Tuan Viet Nguyen, a research scientist from Agriculture Victoria in Australia. They spoke about structural variants, defined as genomic variants larger […]

February 18, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Presentations & Talks, sequencing, Softwares

Accuracy Improvements in Crop Genome Assembly

Tonight, I watched a recording from the Nanopore Community Meeting 2021 featuring Alexander Wittenberg from KeyGene in the Netherlands. They presented “Accuracy improvements in crop genome assembly using the Q20+ chemistry.” KeyGene is a crop innovation company, and they are generating new tools for genome assembly and structural variant analysis, among other analyses. They built […]

Studying Centromere Structure with ONT

I continue to watch the YouTube “Assembly” playlist from the Oxford Nanopore Technologies (ONT) channel. Tonight, I watched session #8! Ian Henderson from the University of Cambridge in the UK presented at the Nanopore Community Meeting 2021. The session was titled “Assembling the centromeres – the ‘black holes’ of the genome.” Henderson said the centromeres […]

February 16, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

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 […]

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

Promoting Community and Biodiversity with Org.one

Tomas Marques-Bonet from the Institute of Evolutionary Biology in Spain spoke about the Org.one project at the Nanopore Community Meeting in 2021. The title of the session was “ORG.one: a new program to promote sequencing biodiversity.” They spoke about the mass extinction of species and the need to preserve biodiversity. Marques-Bonet explained how biodiversity genomics […]

February 14, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

CanSeq150 to Sequence Canada’s Most Endangered Species

The London Calling 2021 session “CanSeq150: high-resolution genomic sequencing and assembly of 150 Canadian species” caught my attention today. Jahanshah Ashkani from Canada’s Michael Smith Genome Sciences Center was the speaker. The goal is to save Canada’s rich biodiversity by sequencing unique species. Loss of biodiversity is an issue: there are over 700 species at […]

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

Sequencing a Fungal Banana Pathogen

Luca Degradi from the University of Milan in Italy presented at London Calling 2021 about “Chromosome-level genome assembly of Fusarium musae using MinION.” They described this organism as a “cross-kingdom pathogen” reported by the HUPLANTcontrol program in Europe. The organism can infect bananas and humans! The first infection seems to have been a human. At […]

January 26, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Metagenomics from Orthopedic Device-related Infections

Teresa Street from the University of Oxford in the UK presented at the Nanopore Community Meeting 2019 on “Metagenomic nanopore sequencing for analysis of orthopedic device-related infection.” Street spoke about the impact of hip, knee, shoulder, elbow, and ankle replacements and the percentage of revisions due to the suspicion of infection. Further surgeries are often […]

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 […]