Brzo preklapanje visoko pouzdanih jednomolekularnih očitanja

undergraduate thesis

• Title (english): Rapid overlapping Single Molecule High-Fidelity Sequencing Data
• Author: Martin Josip Kocijan
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Rafael Josip Penić (član povjerenstva)
• Committee member: Filip Tomas (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2023-07-05, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Pacific Biosciences nedavno je predstavio novi protokol visokopouzdanog sekvenciranja molekula DNA (engl. HiFi), koji omogućuje točne fragmente dugih o\v{c}itanja s minimalnim brojem pogrešaka. Ovaj rad istražuje algoritme koji su manje osjetljivi na pogreške, koristeći vrhunsku točnost i duljinu HiFi podataka. Ovaj pristup uključuje prilagodbu postojećih kao i razvoj novih preklapajućih algoritama prikladnih za paralelizam u C++-u. Dobiveno rješenje ubrzava proces pronalaženja preklapanja fragmenata i preklapanja prema referentnom genomu. Procjenjujemo izvedbu, točnost i učinkovitost ispitanih algoritama, uspoređujući ih sa suvremenim metodama u upotrebi.

Abstract (english)

Pacific Biosciences recently introduced a novel high-fidelity (HiFi) sequencing protocol, enabling accurate long-read fragments with minimal errors. This thesis investigates algorithms that are less error-sensitive, leveraging the superior accuracy and length of HiFi data. This approach involves adapting existing or developing novel overlapping algorithms suitable for parallel architectures in C++. The resulting solution speeds up the process of finding fragment overlaps and mapping against a reference genome. We holistically evaluate the performance, accuracy, and efficiency of the algorithms examined, comparing them to state-of-the-art methods in use.

• Keywords: Bioinformatika; visokopouzdana jednomolekularna očitanja; preklapanje; PacBio
• Keywords (english): Bioinformatics; DNA reads; overlap; PacBio; HiFi
• Language: english
• URN:NBN: urn:nbn:hr:168:950816
• 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: 2023-10-11 09:19:21