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undergraduate thesis
Brzo poravnanje visoko pouzdanih dugačkih očitanja
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2021. urn:nbn:hr:168:170364
Staver, Mauro
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Staver, M. (2021). Brzo poravnanje visoko pouzdanih dugačkih očitanja (Undergraduate thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:170364

Staver, Mauro. "Brzo poravnanje visoko pouzdanih dugačkih očitanja." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2021. https://urn.nsk.hr/urn:nbn:hr:168:170364

Staver, Mauro. "Brzo poravnanje visoko pouzdanih dugačkih očitanja." Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2021. https://urn.nsk.hr/urn:nbn:hr:168:170364

Staver, M. (2021). 'Brzo poravnanje visoko pouzdanih dugačkih očitanja', Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 16 June 2024, https://urn.nsk.hr/urn:nbn:hr:168:170364

Staver M. Brzo poravnanje visoko pouzdanih dugačkih očitanja [Undergraduate thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2021 [cited 2024 June 16] Available at: https://urn.nsk.hr/urn:nbn:hr:168:170364

M. Staver, "Brzo poravnanje visoko pouzdanih dugačkih očitanja", Undergraduate thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2021. Available at: https://urn.nsk.hr/urn:nbn:hr:168:170364

Metadata
TitleBrzo poravnanje visoko pouzdanih dugačkih očitanja
Title (english)Rapid Alignment of High-Fidelity Sequencing Data
AuthorMauro Staver
MentorMile Šikić (mentor)
Committee memberMile Šikić (predsjednik povjerenstva)
Committee memberJosip Marić (član povjerenstva)
Committee memberFilip Bosnić (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2021-07-02, Croatia
Scientific / art field,
discipline and subdiscipline		TECHNICAL SCIENCES
Computing
Abstract
Poravnanje DNA očitanja na referentni genom jedan je od čestih problema u bioinformatici i može biti vrlo težak jer genomi mogu biti vrlo veliki. High Fidelity očitanja imaju zapanjujuću točnost iznad 99% i usku distribuciju duljina sa maksimalnom srednjom vrijednost od oko 25kbp. U ovom radu predstavljamo novi algoritam poravnanja optimiziran za HiFi očitanja, hifimap. Započinjemo sa postavljanjem teoretske podloge algoritma hifimap, zatim razmatramo razne algoritamske detalje i na kraju prezentiramo našu implementaciju. Rezultati su pokazali da hifimap ostvaruje dobre rezultate za male i velike referentne genome, a često i nadmašuje minimap2 koji je smatran industrijskim standardom.
Abstract (english)
Mapping DNA reads to a reference sequence is a common problem in bioinformatics and can be quite hard since sequences are often very large. High Fidelity reads, being the latest advancement in the field, have an astounding accuracy higher than 99% and a narrow length distribution with the maximal mean length of 25k base pairs. In this paper we propose a novel mapping algorithm optimized for HiFi reads, hifimap. We lay the theoretical foundations of the hifimap algorithm, discuss various algorithm details and present our implementation. Results show that hifimap performs well on both small and large reference sequences and in many cases outperforms minimap2 which is considered the industry standard.
Keywords
Keywords (english)
Languageenglish
URN:NBNurn:nbn:hr:168:170364
Study programmeTitle: 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 resourceText
File originBorn digital
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Created on2023-01-14 21:41:08