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Showing 1 to 20 of 86 for “"genome assembly"”.

  1. Improving genome assembly by identifying reliable sequencing data

    2014

    De novo Genome assembly and k-mer frequency counting are two of the classical prob- lems of Bioinformatics. k-mer counting helps to identify genomic k-mers from sequenced reads which may then inform read correction or genome assembly. Genome assembly has two major subproblems: contig construction …

    rutgers

  2. Efficient Algorithms for Prokaryotic Whole Genome Assembly and Finishing

    Biswas, Abhishek2016

    <p>De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) …

    odu Repository record

  3. Error Correction and de novo Genome Assembly of DNA Sequencing Data

    Molnar, Michael ZThe University of Western Ontario2017

    … of DNA determint the sequence of bases in the genome of any species. This information is key in understanding many of the aspects of how life functions. The accuracy of sequencing is extremely important since the differences between individuals of the same species are caused by very few …

    uwo Repository record

  4. Chromosome-level genome assembly of Triatoma dimidiata Latreille, 1811 (Hemiptera: Reduviidae: Triatominae)

    Alvarado López, Mateo Andrés, Cantillo-Barraza, Omar, Luna, Nicolás, Hernández, Carolina, Paniz-Mondolfi, Alberto, Ramírez González, Juan DavidUniversidad del Rosario2025

    Triatoma dimidiata es un vector principal de Trypanosoma cruzi, el parásito responsable de la enfermedad de Chagas, que afecta a millones de personas en todo el mundo. Su distribución se extiende desde el centro de México hasta el norte de Ecuador y Perú, con variaciones ecológicas y …

    rosario Repository record

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

    Luo, XiaoUniversität Bielefeld

    Genomes of the same species usually show high diversity due to genetic variations. Most eukaryotes involve multiple copies of genomes, each of which is inherited from one of the ancestors. Whereas prokaryotes, such as virus and bacteria, are prone to form a collection of closely related strains …

    bielefeld Repository record

  6. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors

    Johnson, Jennifer L.University of Illinois at Urbana-Champaign2018

    … Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive, and conventional farm-bred populations to identify genomic regions associated with the response to selection for behavior. Analysis of the resequenced genomes identified 113 …

    uiuc Repository record

  7. Computational methods for single cell RNA and genome assembly resolution using genetic variation

    Heaton, WilliamUniversity of Cambridge2021

    … range of data parameters and sample types. In genome assembly, the recent higher throughput and lower cost of long read sequencing has revolutionized our ability to create reference quality genomes and has revitalized the assembly community. Now, massive efforts are taking place in the Darwin …

    cambridge Repository record

  8. Improving the genome assembly and annotation of the white-tailed deer (Odocoileus virginianus borealis)

    London, Evan W.University of Illinois at Urbana-Champaign2021

    … elements are ubiquitous within 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 …

    uiuc Repository record

  9. INSIGHTS INTO THE GENETIC DIVERSITY OF ASIMINA TRILOBA: A STUDY USING GENOME ASSEMBLY AND POPULATION GENETICS

    FRIEL, JAMESUniversità degli Studi di Milano2023

    … this, we have produced a high-quality reference genome by assembling 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 …

    milano Repository record

  10. Towards cloning of a novel SCN resistance locus using de novo genome assembly and fosmid screening

    Fliege, ChristinaUniversity of Illinois at Urbana-Champaign2015

    … to a distance of 147kb. Through the use of whole genome sequencing with de novo assembly we were able to gain information about the region. In this thesis the assembly data was used along with fosmid sequences from both Sanger sequencing and Illumina reads to gain insight into sequence differences …

    uiuc Repository record

  11. Analysis of the effect of genetic heterogeneity on de novo genome assembly using Xylocopa virginica as a model.

    Tang, HaimengBrock University2021

    … and genetic research, and as a result, de novo genome sequencing and assembly for non-model organisms has now become a common task in genome research. However, the integral properties of a genome such as ploidy, mutations, and repeat content impose issues for current genome assemblers. In this …

    brock Repository record

  12. Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph

    Movahedi Tabrizi, Narjes Sadat2016

    … to sequence and assemble bacterial</p> <p>genomes from a single cell. However, the quality of single cell genome assembly has</p> <p>not yet reached the quality of normal multi-cell genome assembly due to the coverage</p> <p>bias (including uneven depth of coverage and region blackout) and …

    wayne-thes Repository record

  13. Scaling short read de novo DNA sequence assembly to gigabase genomes

    Cook, Jeffrey J.University of Illinois at Urbana-Champaign2011

    … of sequencing, sparking a revolution in whole genome de novo sequencing. 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 …

    uiuc Repository record

  14. Decoding DNA: scalable genome annotation software, generative AI, and application to the cactus pear genome

    Lomas, Johnathan2025

    The annotation of protein-coding genes from a raw genome assembly involves identifying the sequence regions that are transcribed into mRNA transcripts, spliced, and ultimately translated into protein. Thus, genome annotation is a fundamental task that critically supports systems level biological …

    unr Repository record

  15. Genomics and Transcriptomics Analysis of the Asian Malaria Mosquito Anopheles stephensi

    Jiang, XiaofangVirginia Tech2016

    … and mosquito in general. First we reported the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly was produced using a combination of 454, Illumina, and PacBio sequencing. This hybrid assembly method was significantly better than …

    vt Repository record

  16. Chromosome and Genome Evolution in Culicinae Mosquitoes

    Masri, Reem AbedVirginia Tech2021

    … and Rift Valley fevers. Developing high-quality genome assembly for mosquitoes, studying their population structure, and evolution can help to facilitate the development of new strategies for vector control. Studies on Aedes albopitcus as well as on species from the Culex pipiens complex, which …

    vt Repository record

  17. Events that shape genomes

    Schlebusch, Stephen A.Department of Molecular and Cell Biology2018

    … opened up new possibilities for exploring the genomes of non-model organisms. For this thesis, a diverse range of non-model species from both plants and animals were used to identify and answer questions of evolutionary interest in four case studies. In doing so, a wide assortment of …

    cape-town Repository record

  18. Minimizer-space computation

    Ekim, Barış C.Massachusetts Institute of Technology2025

    … show how fundamental biological tasks, such as genome assembly and read mapping, can be significantly accelerated over state-of-the-art methods.

    mit Repository record

  19. COMPARATIVE GENOMICS OF CHEMOSENSORY GENE FAMILIES AMONG MEMBERS OF THE HELIOTHINAE

    Guo, Rong2023

    … produced a novel Illumina short read C. subflexa genome assembly and an improved, highly contiguous C. virescens genome assembly. Due to quality limitations common to short read assemblies, I used our Heliothine genomes to examine the feasibility of reference-assisted assembly, an approach that …

    maryland Repository record

  20. Bioinformatics and Next Generation Sequencing: Applications of Arthropod Genomes

    Zhang, ZaichaoThe University of Western Ontario2017

    … in this thesis describes NGS applications on genome assembly, genome annotation, and comparative genomics, using arthropods as case studies: (1) by sequencing and analyzing the genomes of three Tetranychus spider mites with three completely different feeding behaviors, we uncovered genomic …

    uwo Repository record

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