Procjena očekivanog stupnja potpunosti genoma iz dostupnih očitanja

undergraduate thesis

• Title (english): The Assesment of the Expected Genome Assembly Completness from Available Reads
• Author: Matej Fureš
• 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: 2019-09-17, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Zadatak završnog rada alat je za provjeru mogućnosti sastavljanja genoma za dani skup očitavanja. Alat se radi u svrhu validacije skupa očitanja prilikom sastavljanja genoma te izačuna omjera duljina novo sastavljenog slijeda i početne reference. Problem je riješen korištenjem programskog jezika C++ te alata Minimap i Gepard. U samom programu korišteni su algoritmi Sweep line i BFS za filtraciju podataka, odnosno za obilazak grafa. Implementirano je rješenje zadovoljavajuće riješilo zadani problem, a njegova poboljšanja mogla bi se napraviti drugačijim parametrima pri ocjenjivanju kvalitete mapiranja ili korištenjem drugih alata.

Abstract (english)

The task of this assignment was implementation of a tool capable of testing the capability of assembling genomes from available reads. The tool was made for the purpose of validating sets of reads while assembling genomes and calculating ratios of lengths between original reference and newly made genome. The problem has been solved using programming language C++ and tools like Minimap and Gepard. In the solution we use Sweep line algorithm for data filtration and BFS algorithm for making a path on the graph. The implementation solved our problem to high degree, and eventual upgrades could be made by changing filtering methods or changing the tools that were used.

• Keywords: C++; Minimap; Gepard; mapiranje; očitanje; graf; BFS; algoritam; Python; bash
• Keywords (english): C++; Minimap; Gepard; maping; read; graph; BFS; algorithm; Python; bash
• Language: croatian
• URN:NBN: urn:nbn:hr:168:384714
• 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 18:00:07