De novo sastavljanje genoma vođeno referencom

undergraduate thesis

• Title (english): Task: Reference-Guided de novo Genome Assembly
• Author: Sara Bakić
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Committee member: Robert Vaser (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2019-07-12, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

De novo sastavljanje genoma jedan je od najkompleksijih problema u bioinformatici. Brojni su problemi prilikom sastavljanja genoma, uzrokovani, kako biološkim specifičnostima, tako i greškama u procesu sekvenciranja. Probleme stvaraju takozvana ponavljajuća i kimerna očitanja. U ovom radu prikazano je kako detektiranje kimernih i ponavljajućih očitanja uz prikladna postupanja s njima pomaže ispravnom sastavljanju genoma. Prikazane su poteškoće na koje se nailazi prilikom sastavljanja genoma te... More kako uz postojeće alate minimap2 i Ra i ispravnu detekciju kimernih i ponavljajućih očitanja što bolje sastaviti genom te rezultati testiranja sastavljenosti genoma. Osim toga, pojašnjeni su i formati korištenih podataka te temeljne značajke korištenih alata. Less

Abstract (english)

De novo genome assembly is one of the most complex problems in Bioinformatics. There are many problems, either caused by biological specificities or mistakes made during sequencing process, that complicate de novo genome assembly process. The problems are mainly caused by chimeric and repeating reads. This thesis describes how detecting and annotating chimeric and repeating reads helps the assembly process. Typical issues that occur during the assembly process and how successful existing... More tools Ra and minimap2 with the detection of chimeric and repeating reads assembly the reads are shown. Besides that, thesis describes file formats used in this work and thorough features of used tools. Less

• Keywords: kimerno; ponavljajuće; genom; minimap2; ra; FASTA; FASTQ; PAF; bioinformatika
• Keywords (english): chimers; repeats; genome; minimap2; Ra; FASTA; FASTQ; PAF; Bioinformatics
• Language: croatian
• URN:NBN: urn:nbn:hr:168:127628
• Study programme: Title: Computing; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2020-01-07 16:25:22