Optical maps in guided genome assembly

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Title: Optical maps in guided genome assembly
Author: Leinonen, Miika
Contributor: University of Helsinki, Faculty of Science
Publisher: Helsingin yliopisto
Date: 2019
Language: eng
URI: http://urn.fi/URN:NBN:fi:hulib-202001211103
Thesis level: master's thesis
Degree program: Tietojenkäsittelytieteen maisteriohjelma
Master's Programme in Computer Science
Magisterprogrammet i datavetenskap
Specialisation: Algoritminen bioinformatiikka
Algorithmic Bioinformatics
Algoritmisk bioinformatik
Discipline: none
Abstract: With the introduction of DNA sequencing over 40 years ago, we have been able to take a peek at our genetic material. Even though we have had a long time to develop sequencing strategies further, we are still unable to read the whole genome in one go. Instead, we are able to gather smaller pieces of the genetic material, which we can then use to reconstruct the original genome with a process called genome assembly. As a result of the genome assembly we often obtain multiple long sequences representing different regions of the genome, which are called contigs. Even though a genome often consists of a few separate DNA molecules (chromosomes), the number of obtained contigs outnumbers them substantially, meaning our reconstruction of the genome is not perfect. The resulting contigs can afterwards be refined by ordering, orienting and scaffolding them using additional information about the genome, which is often done manually by hand. The assembly process can also be guided automatically with the additional information, and in this thesis we are introducing a method that utilizes optical maps to aid us assemble the genome more accurately. A noticeable improvement of this method is the unification of the contigs, i.e. we are left with fewer but longer contigs. We are using an existing genome assembler called Kermit, which is designed to accept genetic maps as auxiliary long range information. Our contribution is the development of an assembly pipeline that provides Kermit with similar kind of information via optical maps. The initial results of our experiments show that the proposed genome assembly scheme can take advantage of optical maps effectively already during the assembly process to guide the reconstruction of a genome.

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