Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja

master's thesis

• Title (english): Scaffolding Assembled Genomes with Long Reads
• Author: Ivan Krpelnik
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Damir Seršić (član povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2018-07-05, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

U ovom radu implementiran je alat za produljivanje i povezivanje sastavljenih slijedova u programskom jeziku C++. Alat je nazvan Ezra i potencijalno bi se mogao koristiti za produljivanje i povezivanje u alatu za de novo sastavljanje Rala. Metode produljivanja i povezivanja bi se trebale izvršavati iterativno, ponavljajući proces sve dok ima valjanih produljenja i povezivanja.

Alat je testiran na umjetno generiranim slijedovima napravljenih nasumičnim rezanjem genoma e. coli i na rascjepanim slijedovima sastavljenim alatom Rala nad Pacbio bakterijskim podatkovnim skupovima. Rezultati testiranja pokazuju da je ova metoda valjana za povezivanje slijedova sastavljenih Ralom.
Izvorni kod dostupan je na \url{https://gitlab.com/Krpa/ezra}.

Abstract (english)

In this thesis, a tool for contig extension and gap closing was implemented in C++. The tool is named Ezra and could be used for extension and bridging by de novo assembler Rala. The extension and bridging methods are meant to be run in iterations, repeating the process while it produces valid extensions and bridges.

The tool was tested on artificial fragments made by randomly cutting e. coli genome and on fragmented assembly produced by Rala on Pacbio bacterial datasets.
The results show that this method is valid for reducing the number of contigs produced by Rala.
The source code is available at \url{https://gitlab.com/Krpa/ezra}.

• Keywords: Povezivanje fragmenata; Sastavljanje genoma; Genom; Dugačka očitanja
• Keywords (english): Scaffolding; Assembly; Assemblies; Genome; Long reads
• Language: english
• URN:NBN: urn:nbn:hr:168:295015
• 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: 2019-03-13 22:01:41