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Showing 1 to 20 of 37 for “"Oxford Nanopore"”.

  1. Approaches to mitochondrial genome sequencing using the oxford nanopore minion device

    Thorson, Kelcie C.2017

    … genome sequencing sans PCR using the Oxford Nanopore MinION. Our hypothesis was that results generated from native DNA sequencing would be concordant to sequencing results generated from PCR-enriched libraries. Error-rates of 1.47% (enriched) and 1.26% (native) were observed when …

    tdl Repository record

  2. Caracterización de comunidades virales en muestras fecales de bovinos de la provincia de Ubaté, Cundinamarca, Colombia

    Medina Velasquez, Julián EstebanUniversidad del Rosario2023

    … mediante secuenciación de tercera generación (Oxford Nanopore Technologies). Describimos el viroma de muestras de heces de bovinos a partir de un muestreo no probabilístico a conveniencia de 42 muestras provenientes de tres municipios de la Provincia de Ubaté, Cundinamarca. Utilizamos un …

    rosario Repository record

  3. Mechanism of Permissive Cleavage Activity of TevCas12a

    White, AlexaThe University of Western Ontario2023

    … of the TevCas12a cleavage products with Oxford Nanopore revealed that most of the non-guide directed cuts were within I-TevI’s cleavage motif, indicating that I-TevI is responsible for the cuts. A mechanism is proposed for how I-TevI and Cas12a work together to permissively cleave DNA.

    uwo Repository record

  4. Fast and accurate alignment of barcoded reads

    Shajii, Ariya (Ariya Reza)Massachusetts Institute of Technology2018

    … developed by Pacific Biosciences and Oxford Nanopore accomplish this goal by producing physically longer reads, several other technologies take an alternate route by instead producing "barcoded reads", including 10x Genomics' Chromium platform and Illumina's TruSeq Synthetic Long-Read …

    mit Repository record

  5. Detection of Nucleic Acid Disease Biomarkers Using Solid-State Nanopores

    Zahid, OsamaWake Forest University2017

    Nanopore sensing technology was initiated with the ultimate goal of developing a rapid, single-molecule sequencer. With the release of Oxford Nanopore Technology’s Minion sensor in 2014, that goal has been achieved. While this device utilizes biological nanopores, Solid-State Nanopore sensors were …

    wfu Repository record

  6. Identifying and Tracking the Evolution of Mutations in the SARS-CoV-2 Virus

    Venkatesan, LavanyaVirginia Tech2021

    … exploits the data generated by the Illumina and Oxford Nanopore next generation sequencing methods to study the evolution of mutations in a single Septuagenarian patient over an infection period of 102 days using the gene analysis software Geneious Prime.

    vt Repository record

  7. Mixed Strain Identification of Porcine Reproductive and Respiratory Syndrome Virus in Multiplexed Samples using Nanopore Sequencing

    Buman Ruiz Diaz, Maria PazVirginia Tech2024

    … rapid turnaround time and long-read capacity of Oxford Nanopore Technology's MinION next-generation sequencer. We have developed a novel primer set designed to span Open Reading Frames 3 through 7 of the PRRSV genome, which has allowed for multiplexing of samples, thus reducing individual cost of …

    vt Repository record

  8. Computational methods for the detection of somatic structural variants in cancer genomes using long-read sequencing

    Elrick, HillaryUniversity of Cambridge2024

    … regions, SV types, and sizes. Using Illumina and Oxford Nanopore whole-genome sequencing data from 99 tumours and matched normal samples of patients, I show that SVs reported by SAVANA are highly concordant with those detected using short-read sequencing, including in regions of complex structural …

    cambridge Repository record

  9. A sequencing-based analyisis of epigenetic modifications of the mitochondrial genome

    Bicci, IacopoUniversity of Cambridge2022

    … identification using long-read based technology Oxford Nanopore Sequencing. Our approach circumvents mtDNA-specific confounders, while enriching for native full-length molecules over nuclear DNA. Variant calling analysis against Illumina deep re-sequencing showed that all expected mtDNA variants …

    cambridge Repository record

  10. Read alignment using deep neural networks

    Shrestha, Akash, author, Chitsaz, Hamidreza, advisor, Ben-Hur, Asa, committee member, Abdo, Zaid, committee memberColorado State University. Libraries2019

    … marketed sequencing technologies are Oxford Nanopore and PacBio SMRT sequencing, which are considered top players because of their extremely long reads and low cost. However, the reads may contain error up to 20% that are not generally uniformly distributed. To deal with that level of …

    colostate Repository record

  11. Análisis Metagenómico del Viroma Intestinal en Pacientes Intrahospitalarios y de Unidad de Cuidados Intensivos de Bogotá, Colombia

    Ramírez Hernández, Angie LorenaUniversidad del Rosario2024

    … saludables (n=14), utilizando secuenciación por Oxford Nanopore Technologies (ONT) e Illumina. En promedio, se obtuvo 161,855 lecturas por muestra usando secuenciación por ONT, de las cuales cerca del 0,03% correspondió a lecturas virales. Para el caso de Illumina, se obtuvo alrededor de …

    rosario Repository record

  12. GENETIC DISSECTION OF MATURITY DATE IN PEACH AND APRICOT REVEAL A ROLE FOR CONSERVED GENE NETWORKS

    TAGLIABUE, ALESSANDRO GIULIOUniversità degli Studi di Milano2026

    … refined, then combined Illumina short-read and Oxford Nanopore long-read sequences have been used to characterize the structural variations of the region. In chapter 3 QTls associated to MD have been identified in the segregating population ‘BO96621030 x Harostar’. By combining different …

    milano Repository record

  13. Exploring the genetic landscape in cutaneous T-cell lymphoma with short- and long-read sequencing

    Hain, CarstenUniversität Bielefeld

    … altered copy-number landscape. The use of Oxford Nanopore long-read sequencing enabled a precise elucidation of structural variants and uncovered multiple classes of complex structural variants underlying the recurrent losses of common tumor suppressor genes in mycosis fungoides.<br /> In …

    bielefeld Repository record

  14. Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa

    Ho, Yi-TingDepartment of Biological Sciences2023

    … sequencing) as well as their metagenomes (Oxford Nanopore Technologies). ChromasPro and seaview.exe were used for sequence analysis and tree building, respectively. MGnify and Flye were used for assessing the metagenomics of selected samples. Parsimony-based tree fitting was generated for …

    cape-town Repository record

  15. Computational Methods for Haplotype-aware De Novo Genome Assembly from Long Reads

    Luo, XiaoUniversität Bielefeld

    … technologies such as Pacific Biosciences and Oxford Nanopore Technologies, have greatly improved haplotype phasing and genome assembly because of the tremendous advantages in terms of read length. Nevertheless, the vast majority of existing long-read haplotype phasing or genome assembly tools …

    bielefeld Repository record

  16. Characterizing the Microbiome of Scottish Freshwater Pearl Mussels (Margaritifera margaritifera): A Metabarcoding Analysis using Next-Generation Sequencing

    MacCallum, Alanna-JoUniversity of the Highlands and Islands2025

    … sequencing platforms were utilized: the MinION (Oxford Nanopore Technology) for full-length amplicons and MiSeq (Illumina) for short amplicons, enabling a comparative analysis of platform performance at the species level. Results revealed that the mussel microbiome was distinct from that of river …

    uhi-uk Repository record

  17. Integrating bioinformatic approaches to promote crop resilience

    Cui, ChenmingVirginia Tech2019

    … for combining long-read sequencing from the Oxford Nanopore Technologies MinION, and short-read data, to rapidly assembly a cost-effective, contiguous and relatively complete genome. Here we uncovered hidden variation in a well-known plant pathogen finding that the genome was 92% bigger than …

    vt Repository record

  18. Genetic diversity of sars-cov-2 in southern province of Zambia.

    Katowa, BenThe University of Zambia2022

    … using the CDC protocol (Lu et al., 2020). The Oxford Nanopore and Nextseq illumina platforms were used for WGS. From the 198 samples collected, a total of 40 whole genomes were sequenced. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta …

    zimbabwe Repository record

  19. Genetic diversity of sars-cov-2 in southern province of Zambia.

    Katowa, BenThe University of Zambia2022

    … using the CDC protocol (Lu et al., 2020). The Oxford Nanopore and Nextseq illumina platforms were used for WGS. From the 198 samples collected, a total of 40 whole genomes were sequenced. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta …

    zambia Repository record

  20. The broken genome: Merging cutting edge technologies for a molecular understanding of the Flock House virus defective interfering particle.

    Jaworski, Elizabeth AThe University of Texas Medical Branch at Galveston2022

    … events with nucleotide resolution) and Oxford Nanopore Technologies’ MinION (to characterize full-length and defective genomes) I have characterized the step wise progression of DI-RNA formation and the species distribution of these genomes. I observed a rapid accumulation of mature …

    utmb Repository record

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