The impact of third generation sequencing on haplotype assembly

Doctoral thesis (2024)

Authors

R. Shirali Hossein Zade Pattern Recognition and Bioinformatics - EEMCS
Research Group
Pattern Recognition and Bioinformatics (EEMCS) (TU Delft)
Copyright: © 2024 R. Shirali Hossein Zade
DOI
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https://doi.org/10.4233/uuid:16494021-9bd2-4089-8808-5ad9dffadc5d
Haplotype assembly Genome assembly Third generation sequencing Genome repeats
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Published Date

2024

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Department

Intelligent Systems

Research Group

Pattern Recognition and Bioinformatics

Abstract

The genome encompasses an organism’s full DNA, organized into chromosomes within the cell nucleus. Humans have 46 paired chromosomes, and within these pairs, genetic information is grouped as haplotypes—genetic packages passed from one generation to the next, ensuring genetic diversity. While DNA sequencing produces short fragments or reads, assembling these back into a complete genome can be complex. The presence of multiple, similar haplotypes in some organisms amplifies this complexity, emphasizing the need for specialized techniques to accurately capture these subtle genetic variations.
In this thesis, we dive into the de novo and haplotype assembly challenges. We aim
to tackle haplotype assembly challenges and find better ways to accurately assemble the genetic puzzle pieces. Along the way, we introduce a new tool for haplotype assembly designed to make the process more interpretable.