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 32 for “"short reads"”.
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Evaluating and Improving Performance of Bisulfite Short Reads Alignment and the Identification of Differentially Methylated Sites
Large-scale bisulfite treatment and short reads sequencing technology allows comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype …
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Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
… RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is …
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Computational methods for the detection of somatic structural variants in cancer genomes using long-read sequencing
… are highly concordant with those detected using short-read sequencing, including in regions of complex structural variation. I also highlight the enhanced ability of long-reads to identify SVs in repetitive regions where short-reads are unable to map with high confidence. In summary, this thesis …
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A Parameterization Study of Short Read Assembly Using the Velvet Assembler
… large, contiguous sections of genetic code from short reads generated from laboratory techniques. We explore the Eulerian Path approach in detail, utilizing a de Bruijn Graph, and demonstrate current software technologies and algorithms using a sample genome. We investigate the input parameters …
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RNA CoMPASS: RNA Comprehensive Multi-Processor Analysis System for Sequencing
… experiments generate hundreds of millions of short reads for each DNA/RNA sample. There are many existing bioinformatics tools developed for the analysis and visualization of this data, but very large studies present computational and organizational challenges that are difficult to overcome …
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Computational approaches to stochastic systems in physics and biology
… I analyze the raw data for this research, namely short reads of 16S ribosomal RNA, and quantify how much of phylogenetic information is lost by using these short reads instead of full-length reads, and show that for lengths spanning 300 to 400 base pairs, we can recover some meaningful …
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Identifying and Analyzing Indel Variants in the Human Genome Using Computational Approaches
… indels than existing algorithms. While mapping short reads to the reference genome, a significant number of short reads are unmapped and excluded from downstream analyses, thereby causing information loss in the subsequent variant calling. This dissertation describes Genesis-indel, a …
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Performance comparison of five RNA-seq alignment tools
Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data …
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Development of new tools and applications for high-throughput sequencing of microbiomes in environmental or clinical samples
… by providing a very large number of short reads at a significantly lower cost per base pair (bp) than conventional longer-read systems like the Roche-454 GS FLX pyrosequencing instrument. Short-read platforms, however, are not readily amenable to some applications like metagenomics …
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A GPU program to compute SNP-SNP interactions in genome-wide association studies
… in the next generation sequencing technologies, short read sequences of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to …
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Scaling short read de novo DNA sequence assembly to gigabase genomes
… However, these new technologies sample much shorter segments of DNA, called short reads, than conventional but more costly long read sequencing technologies, and suffer from higher and more varied error rates. Modern genome assembly tools compensate for these shortcomings by using de Bruijn …
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A pan-genome wide association study to identify genes associated with invasive Streptococcus pneumoniae
… approach using whole-genome sequencing short reads of 1477 samples from Malawi, including those obtained from the nasopharynx of carriers (825 samples) and from the blood and cerebrospinal fluid of patients (652 samples). In-silico serotyping identified 56 serotypes in the cohort and …
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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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Improving the genome assembly and annotation of the white-tailed deer (Odocoileus virginianus borealis)
… mammalian genomes, and long single-molecule reads produced by third-generation sequencing can span these regions. I present a genome produced with DNA from a single white-tailed deer sequenced on the PacBio Sequel II platform and assembled using Redbean (WTDBG2) long-read assembly software. …
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Bacterial genes and genome dynamics in the environment
… 2, I design a new hybrid assembly approach for short reads and assemble 82 Vibrio genomes. Using the ecologically defined groups of this bacterial family, I investigate the genomic and metabolic correlates of habitat and differentiation, and evaluate a neutral model of gene content. In Chapter …
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Metagenomic approaches for examining the diversity of large DNA viruses in the biosphere
… simulator (CAMISIM) to generate simulated short reads with known composition to assess these processes. Moreover, I emphasized the importance of binning contigs for viral genomes to fully recover the genomes of viruses along with discussing how diversity metrics were differed for contigs, …
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Taxonomic classification of metagenomic sequences
… In the last experiment we show that also very short reads can, in principle, be used to describe the taxonomic content of a metagenome.
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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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Approaches to understanding diversity in rubber and carotenoid synthesis in <i>Hevea brasiliensis </i>latex
… reference 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 …
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Towards a Pangenome Perspective on the Lake Malawi Cichlid Radiation
… most of these findings were based on aligning short reads to a single linear reference genome, which has the limitation of ignoring larger scale structural variation that has great potential to cause alterations to phenotype. To better address this question, I adopt a pangenomic approach by …
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