Mapiranje dugačkih očitanja

undergraduate thesis

• Title (english): Long Reads Mapping
• Author: Kristijan Pongračić
• 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

Mapiranje dugačkih očitanja jest problem pronalaska dijela reference na koje bi se konkretno očitanje moglo najbolje poravnati. U ovom radu opisana je implementacija programa koji mapira dugačka očitanja. Program je napisan u programskom jeziku C++. Koristi se pristup u kojem se ne gleda cijelo očitanje, već samo krajevi duljine K. Referenca se podijeli na regije duljine 2K s preklapanjem od K te se indeksira. Indeksiranjem krajeva očitanja te usporedbom s indeksima na referenci mogu se brzo... More filtrirati kandidatne pozicije. Rezultati su uspoređeni s Minimap2 metodom. Izvorni kôd dostupan je na https://github.com/lbcb-edu/BSc-thesis-18-19/tree/kpongracic. Less

Abstract (english)

Long reads mapping is problem of finding a part of a reference on which a particular read could be best aligned. This paper describes the method for long reads mapping. It was written in C++ programming language. In our approach instead of whole read we use only read ends of length K for finding candidate positions on the reference genome. The reference is divided into regions of length 2K with overlapping of K and is beeing indexed. By indexing the reads ends and by comparing the indexes... More with references, the candidate positions can be filltered quickly. The results are compared with the Minimap2 tool. Source code is available at https://github.com/lbcb-edu/BSc-thesis-18-19/tree/kpongracic. Less

• Keywords: bioinformatika; mapiranje; dugačka očitanja; Minimap2
• Keywords (english): bioinformatics; mapping; long reads; Minimap2
• Language: croatian
• URN:NBN: urn:nbn:hr:168:013217
• 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 21:28:58