Brzo preklapanje visoko pouzdanih jednomolekularnih očitanja

master's thesis

• Title (english): Rapid overlapping of Single Molecule High-Fidelity Sequencing Data
• Author: Suzana Pratljačić
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Ana Sović Kržić (član povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2021-07-09, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Tvrtka Pacific Bioscience 2019. godine predstavila je novu tehnologiju sekvenciranja visoko pouzdanih fragmenata koja kombinira koncepte korištene za sekvenciranje tradicionalnih kratkih i dugačkih očitanja s greškama. Visoko pouzdani fragmenti karakterizirani su velikom duljinom i visokom točnosnu. Činjenica da podatci imaju jako mali broj grešaka može se koristiti za osmišljavanje algoritama koji su manje osjetljivi na pogreške. U ovom radu predstavit ćemo algoritam za mapiranje visoko pouzdanih fragmenata. Algoritam koristi sufiksno polje i seed-chain-align proceduru. Analizirat ćemo performanse i točnost razvijenog alata i usporediti ga sa suvremenim algoritmima za mapiranje.

Abstract (english)

In 2019, Pacific Bioscience introduced highly accurate long-read sequencing (HiFi sequencing), a paradigm that combines concepts from traditional short and long error-prone reads technologies. Long lengths and high base-level resolution characterize the HiFi fragments. These characteristics can be utilized to design algorithms that are less sensitive to errors. In this article, we present the novel algorithm for HiFi reads mapping. The algorithm is based on suffix arrays and a standard seed-chain-align procedure. We will analyze the performance and accuracy of the developed tool and compare it to state-of-the-art algorithms.

• Keywords: Visoko pouzdana jednomolekularna ocitanja; sufiksno polje
• Keywords (english): HiFi PacBio reads; DNA sequencing; suffix array
• Language: english
• URN:NBN: urn:nbn:hr:168:100082
• Study programme: Title: Computing; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2023-01-13 13:33:15