Softwares

May 30, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Bambu for Transcript Discovery

Andre Sim from the Genome Institute of Singapore (A*STAR) in Singapore spoke at the Nanopore Community Meeting 2021 about “Bambu – generating context-aware transcriptomes with Oxford Nanopore long-reads.” What a cool name! Sim explained that RNA sequencing technologies have evolved, but reference annotation for transcript analysis has remained relatively unchanged. Sim noted that fragments could […]

Rapid-CNS2

Tonight I watched the Nanopore Community Meeting 2021 recording featuring Areeba Patel and titled “Rapid-CNS2: rapid, comprehensive adaptive nanopore sequencing of central nervous system (CNS) tumours.” Patel is at the German Cancer Research Center (DKFZ) and the University Hospital Heidelberg, Germany. Patel spoke about the use of molecular diagnostics for CNS tumors. They noted the […]

May 28, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares, Undergraduate Research

Portable GPUs

Miles Benton from the Institute of Environmental Science and Research in New Zealand spoke at the Nanopore Community Meeting 2021 about “Affordable GPU compute makes nanopore sequencing even more disruptive and empowering.”Benton is a senior scientist, bioinformatician, and an advocate of open, reproducible science. They share their materials on GitHub. Benton spoke about the birth […]

May 26, 2023
By Carlos C. Goller
Information Literacy, Oxford Nanopore Technologies, Reflections, sequencing, Service Learning, Softwares, Student groups, Undergraduate Research

Undergraduate Research with the CREWS Project

Megan Radosevich from Carroll College presented at the Nanopore Community Meeting 2021 on “Analyzing regional and seasonal microbial community variation from a contaminated Montanana river.” Their project is called CREWS: Consortium for Research on Environmental Water Systems that is funded by the Montana NSF EPSCoR Partnership with several colleges and universities in Montana. A central […]

May 24, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Raw Read Accuracies and Genome Assembly

Alexander Wittenberg from KeyGene in the Netherlands presented at the Nanopore Community Meeting 2021 on “Accuracy improvements in crop genome assembly using the Q20+ chemistry.” They presented on improvements in sequencing and crop assembly using Q20+ chemistry. KeyGene is using genome assembly and the early access ONT program to identify pan-genome and variants. KeyGene has […]

May 23, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Allele-specific Methylation in Fishes

Henri van Kruistum presented at the Nanopore Community Meeting 2021 on “Allele-specific DNA methylation in the live-bearing fish Poeciliopsis gracilis.” Kruistum is a Ph.D. student at Wageningen University in the Netherlands. They are working on the Poecillidae live-bearing fishes. There are sever species and on the genomic level there is interest in learning about the […]

May 21, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Real-time Sequencing of Brain Samples

Franz-Josef Müller & Helene Kretzmer gave a presentation at the Nanopore Community Meeting 2021 about “Real-time cancer classification with nanopore sequencing.” Kretzmer defined real-time sequencing as “short time” sample processing from wet lab to bioinformatics. Muller explained that they have optimized a protocol for identification of brain cancers. They start with a rapid DNA extraction […]

May 17, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Genomic Skimming on the MinION

I continue to watch Nanopore Community Meeting 2021 recordings and will spend some time later this week focusing on the London Calling 2023 Masterclasses. Tonight, I watched Joanna Malukiewicz from the German Primate Center present on “Genomic skimming on the MinION uncovers cryptic hybridization in the buffy-tufted marmoset, one of the world’s most threatened primates.” […]

May 16, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Org.one Collaborations for Sequencing Biodiversity

Tomas Marques-Bonet from the Institute of Evolutionary Biology in Spain presented at the Nanopore Community Meeting 2021 about “Org.one: a new program to promote sequencing biodiversity.” Tomorrow London Calling 2023 begins and I am continuing to watch previous sessions. Marques-Bonet highlighted how biodiversity is at risk, with more than 37,400 species threatened with extinction. Amphibians […]

May 15, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

The Biological Implications of DNA and RNA Modifications

Ewan Birney from EMBL & EMBL-EBI in the UK presented at the Nanopore Community Meeting 2021 on “DNA and RNA modifications: how nanopore is giving us new biological insights -from COVID to gene expression.” They began by explaining that nanopore sequencing and sensing modification was recognized as feasible in 2014. DNA modifications such as CpG […]