Brzo poravnanje visoko pouzdanih dugačkih očitanja

undergraduate thesis

• Title (english): Rapid Alignment of High-Fidelity Sequencing Data
• Author: Mauro Staver
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Josip Marić (član povjerenstva)
• Committee member: Filip Bosnić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2021-07-02, 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: Mapiranje; Poravnanje; Hifi očitanja; PacBio; hifimap; minimap2
• Keywords (english): Mapping; Alignment; HiFi reads; PacBio; hifimap; minimap2
• Language: english
• URN:NBN: urn:nbn:hr:168:170364
• 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: 2023-01-14 21:41:08