Genome assembly and quality control for non-model organisms

Clavijo, Bernardo (2019) Genome assembly and quality control for non-model organisms. Doctoral thesis, University of East Anglia.

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Abstract

This thesis presents my work in genome assembly between 2010 and 2019.

Chapter 1 is an introduction to the status of the field, presenting the challenges and opportunities on generating de novo genome assemblies. Chapter 2 presents the development of k-mer spectra validation for assembly completeness, from its beginnings as unique sequence coverage analyses, through its implementation in the Kmer Analysis Toolkit, up to its use to assess consensus accuracy on hybrid assemblies. Chapter 3 describes a series of objective guided de novo assembly strategies applied to non-model genomes, starting with the assembly of the medicinal plant C. roseus to investigate its biosynthesis pathways, continuing with the chromosome-scale assembly of the ash dieback fungus during the UK outbreak, and concluding with my work assembling the hexaploid wheat genome from whole genome shotgun short read data. Chapter 4 describes the creation of haplotype-collapsed assemblies for 16 specimens of Heliconius butterflies to enable evolutionary analyses, and presents the Sequence Distance Graph framework to work with genome graphs and multi-technology data integration as a step towards haplotype-specific assemblies. Finally, Chapter 5 discusses this research and its impact in the context of the present and future of the field.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	19 Oct 2022 12:30
Last Modified:	19 Oct 2022 12:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/89204
DOI:

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