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 28 for “"PacBio"”.
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Understanding The Mechanism and Extent of Vlse Recombination In Borrelia Burgdorferi Using Next-Generation Sequencing
… those from mice infected for 7 days. Analysis of PacBio single molecule real-time (SMRT) sequencing indicated the presence of 0.84% to 1.18% variants in pure<em> in vitro </em>cultures and 0.79% to 1.22% in tissue explants, as compared 36% to 57% for organisms from mouse bladder tissue 7 days post …
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Genetic variation in the IFITM locus and its phenotypic consequences
… and single molecule, real-time sequencing (PacBio RS). Conventional pulldown protocols for targeted sequencing have not been designed for single molecule, real-time sequencing at the time, thus in Chapter 3, I provide some details of the optimisation work required to adapt the targeted …
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Next-Generation Approaches to Understanding the Diversity and Evolution of Marine Fungi
… Using a third-generation sequencing technology, PacBio circular consensus sequencing, which trades the high coverage of other sequencing platforms for much longer read lengths, I target an approximately 2kb fragment of the ribosomal DNA operon that contains both the full fungal internal …
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Comprehensive evaluation of error correction methods for high-throughput sequencing data
… read sets from technologies like Illumina, PacBio and ONT. The performances of 23 different error correction tools have been analyzed using SPECTACLE and the compiled datasets. This thesis also provides unique and helpful insights into the strengths and weaknesses of various error correction …
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Read alignment using deep neural networks
… 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 error rate and read …
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A Population Genomic Study of Mutton Snapper (Lutjanus analis) Throughout Florida and the Caribbean
… score of 93.3% was developed using Illumina and PACBio sequencing combined with Hi-C scaffolding and applied in population genomic analysis. Mutton snapper (total sample size 724) were collected between 2021 and 2025 from coastal waters off Belize, Puerto Rico, St. Thomas, Martinique, and three …
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Development of a multi-omics approach to identify highly correlated transcriptomic, proteomic and metabolic signatures in maize B73 and FR697 drought stressed nodal roots
… an annotated "SuperTranscriptome" assembly from Pacbio Iso-Seq and RNA-Seq datasets to serve as a representative assembly for the FR697 genotype. The results were incorporated into the KBCommons maize database for storage and analysis from various viewpoints. To visualize interactions between the …
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Improving the genome assembly and annotation of the white-tailed deer (Odocoileus virginianus borealis)
… from a single white-tailed deer sequenced on the PacBio Sequel II platform and assembled using Redbean (WTDBG2) long-read assembly software. Post-assembly, long and short reads from the same animal were used for error-correcting and polishing the assembly. Gene models were predicted with the …
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Genomics and Transcriptomics Analysis of the Asian Malaria Mosquito Anopheles stephensi
… using a combination of 454, Illumina, and PacBio sequencing. This hybrid assembly method was significantly better than assemblies generated from a single data source. A total of 11,789 protein-encoding genes were annotated using a combination of homology and de novo prediction. Secondly, we …
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Chromosome-level genome assembly of Triatoma dimidiata Latreille, 1811 (Hemiptera: Reduviidae: Triatominae)
… integrando lecturas de alta fidelidad de PacBio (HiFi), secuenciación Illumina de extremos emparejados, Hi-C y RNAseq. Los ensamblajes resultantes, con longitudes de 1,31 Gb y 1,30 Gb, demuestran alta completitud y continuidad. Aproximadamente, el 95% de estas secuencias fueron organizadas …
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Co-linear Chaining on Graphs With Cycles
… significantly in the task of aligning real human PacBio data. GraphChainer is freely available as an open source tool at https://github.com/algbio/GraphChainer.
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Next-Generation Sequencing of vlsE Recombinational Switching in the Lyme Spirochete
… a new assay for switching at vlsE based on PacBio sequencing and an analytical pipeline that allows the analysis of tens of thousands of full-length variants. We developed the first fully-automated and unbiased method to accurately identify switch events and non-templated mutations from …
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Characterization of the sex chromosomes in spinach
… selected by SpoX was sequenced at 63X using PacBio. Sequence data was assembled into an 823 Mbp assembly using CANU so the YY assembly could be compared to a 911 Mbp XX assembly. Seven genes that were non-repetitive sequences were found on a 1.14 X-specific contig from the XX assembly, and …
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The Epstein-Barr Virus-Encoded BHRF1 miRNAs Regulate Viral Gene Expression in Cis
… a meta-analysis of RNA-Seq data and performed PacBio sequencing to show that splicing from EBNA-LP to the HF exon, which contains the BHRF1-2 and 1-3 pri-miRNAs, occurs at a high frequency. This had not been previously established due to the limitations of short reads used in RNA-Seq analysis. …
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Caste-Specific Expression Of Coding And Noncoding Genes In Ant Brains
… the contiguity of the Harpegnathos genome using PacBio long-read sequencing technology, enabling the annotation of lncRNAs and identification of caste-, brain-, and developmental stage-specific lncRNAs. The biochemically focused second section discusses development of a method called MapR to …
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Identification and Characterization of Y Chromosome and M Locus Genes in Anopheles and Aedes Mosquitoes Using the Chromosome Quotient Method
… of the Anopheles gambiae Y chromosome using PacBio sequencing and the CQ method. We discovered that 92.3 percent of predicted Y sequences fell into two classes, the zanzibar amplified region (ZAR) and the satellite amplified region (SAR). This analysis fills in a large piece of the Anopheles …
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Pseudoscorpion Systematics & Phylogenetics: Exploring the Effects of Accelerated Rates of Evolution on Both Ancient and Recent Diversification
… 1790), assemble the first chthoniid genome using PacBio HiFi long reads, and compare the general genome architecture and composition to the genome of the chernetid pseudoscorpion Cordylochernes scorpioides (Linnaeus, 1778).
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Investigating the genome complexity of Streptomyces clavuligerus
… of short-read Illumina sequencing and long-read PacBio technology. Additionally, the telomeres of the five replicons were purified by a self ligation method, and identification of the sequences confirmed that the five replicons carry archetypal telomeres, with the chromosome and megaplasmid …
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The Convoluted Origin and Diversification of Strangler Figs in the Neotropics
… DNA reads from three sequencing platforms (PacBio Sequel II, Nanopore MinIon, and Illumina Miseq). With this data I was able to assemble 92% of the F. velutina genome. 56.4% of the genome was annotated with either gene predictions or repetitive elements. I also explore the applicability of …
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Identification of quantitative trait loci, candidate genes and diagnostic markers for Hessian fly resistance in wheat
… of Overland (Overland v1.1) 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 …
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