Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 26 for “"Long reads"”.
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Computational Methods for Haplotype-aware De Novo Genome Assembly from Long Reads
… different haplotypes. Over the last few years, long-read sequencing 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 …
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1q21.1 syndrome: A perspective on Structural Variant detection & the evolutionary profile of associated protein domains
… requiere tecnologías de secuenciación basadas en long reads para poder genotipar a sus pacientes de forma precisa. Además, 1q21.1 comprende múltiples duplicaciones segmentarias, tales como los dominios Olduvai, asociados con macro- y microcefalia. El primer objetivo de este estudio es diseñar un …
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Long read mapping at scale: Algorithms and applications
… in sequencing due to the development of long and ultra-long read sequencing technologies by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). Long reads are attractive because they narrow the scale gap between sizes of genomes and sizes of sequenced reads, with the …
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Computational methods for the detection of somatic structural variants in cancer genomes using long-read sequencing
… method for the analysis of somatic SVs using long-read whole genome sequencing data from tumours and matched normal samples. SAVANA employs machine learning to distinguish true somatic SVs from germline events and noise. Additionally, I establish best practices for benchmarking SV detection …
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De Novo Assembly of Genomes in Microbiomes: From Amplicons to Whole-Genome Shotgun Sequencing
… errors in third-generation sequencing (TGS) reads by leveraging NGS reads? Finally, how can we better integrate the strengths of NGS and TGS to enable strain-aware metagenome assembly?<br /><br /> To evaluate the robustness of mainstream bioinformatics pipelines in analyzing 16S rRNA gene …
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Read alignment using deep neural networks
… 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 error rate and read length, proximity preserving hashing techniques, such as Minhash and Minimizers, …
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Error correcting optical mapping data
… with insertion and deletions in the alignment of long reads. Moreover, they are arguably harder since the data is integral and susceptible to inaccuracy. We develop cOMet to tackle error correct Rmap data, which to the best of our knowledge is the is the only non-proprietary error correction …
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Legume-rhizobia interactions in a complex microbiome
… the substrate at detectable levels. The use of long reads with the MinION DNA sequencer also allowed the potential of identification of horizontal gene transfer events. None were detected in an initial screen, but a framework for further inspection of this dataset for such events is described.
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Legume-rhizobia interactions in a complex microbiome
… the substrate at detectable levels. The use of long reads with the MinION DNA sequencer also allowed the potential of identification of horizontal gene transfer events. None were detected in an initial screen, but a framework for further inspection of this dataset for such events is described.
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Engineered Replicases, Synthetic DNA, and Long-Read Sequencing Quality Control for Adeno-Associated Virus Production
… as the model. Unlike previous methods, the long reads and low bias of the direct nanopore sequencing technology readily revealed recombination events while also allowing for the quantification of adverse packaging. 2 – 3% of packaged genomes of the tested rAAV carried non-transgene …
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INSIGHTS INTO THE GENETIC DIVERSITY OF ASIMINA TRILOBA: A STUDY USING GENOME ASSEMBLY AND POPULATION GENETICS
… a draft genome using PacBio's Sequel II long reads and polishing with Illumina short reads. We first used a genotype-by-sequencing (GBS) to genotype 124 individuals from 28 sites across the state of Virginia to produce a set of single nucleotide polymorphisms (SNPs). We then analysed the …
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UNCOVERING LNCRNA-CHROMATIN INTERACTIONS SHAPING HUMAN MONOCYTE TO MACROPHAGE DIFFERENTIATION
… of most chromatin-associated RNAs, particularly long non-coding RNAs (lncRNAs), are still being elucidated, with new functions continuously emerging as the filed advances. In recent years, several technologies have been developed to study RNA-chromatin interactions at a genome-wide scale, …
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Expanding Genetic and Genomic Resources for Sex Separation and Mosquito Control Strategies
Mosquitoes belonging to the genera Anopheles transmit malaria parasites, attributing the highest mortality of any vector-borne disease worldwide. Mosquitoes belonging to the genera Aedes transmit arboviruses including dengue, which has become the most important vector-borne virus due to a drastic …
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Computational Tools for Annotating Antibiotic Resistance in Metagenomic Data
… can generate millions of short sequencing reads that are processed by computational tools. However, with the rapid adoption of metagenomics a large amount of data has been generated. This situation requires the development of computational tools and pipelines to manage the data scalability, …
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Pseudoscorpion Systematics & Phylogenetics: Exploring the Effects of Accelerated Rates of Evolution on Both Ancient and Recent Diversification
… order Pseudoscorpiones De Geer, 1778 evolved long enough ago to be present for the coming together and breaking apart of the supercontinent Pangea, the rise and fall of the Dinosaurs, and many iterations of extreme global climatic fluctuations. Roughly 400 million years of diversification and …
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Approaches to understanding diversity in rubber and carotenoid synthesis in <i>Hevea brasiliensis </i>latex
… transcripts was constructed by merging short-reads (RNA-seq) and long-reads (Iso-seq and full-length cDNA sequences) data from <i>Hevea brasiliensis</i>. This produced a comprehensive set of 193,997 transcript sequences with good level of coverage of predicted transcripts and highly conserved …
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A pan-genomics approach linking genotype and phenotype in the mega-pest, Helicoverpa armigera
… in sequencing technologies, specifically long-read sequencing, have dramatically improved the resolution of the genetic information able to be gained from individuals. This information enables the application of pan-genomic approaches (which are focused on assessing the large-scale …
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A pan-genomics approach linking genotype and phenotype in the mega-pest, Helicoverpa armigera
… in sequencing technologies, specifically long-read sequencing, have dramatically improved the resolution of the genetic information able to be gained from individuals. This information enables the application of pan-genomic approaches (which are focused on assessing the large-scale …
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Identification of quantitative trait loci, candidate genes and diagnostic markers for Hessian fly resistance in wheat
… was generated using PacBio high-fidelity (HiFi) long reads. Screening of over 8,000 plants with the flanking markers identified 36 critical new recombinants in the H35 interval. With 12 newly developed kompetitive allele specific PCR (KASP) markers, H35 interval was finely mapped to a 38 kb …
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Convergent evolution of betalains in Caryophyllales
… assemble three new Caryophyllales genomes with long reads. Two key genes of the betalain pathway are clustered in the Beta vulgaris genome, and I use comparative genomics to explore the evolutionary history of this clustering. Strikingly, I show that a pattern dispersed synteny of …
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