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master's thesis
Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2018. urn:nbn:hr:168:295015
Krpelnik, Ivan
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Krpelnik, I. (2018). Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja (Master's thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:295015

Krpelnik, Ivan. "Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja." Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2018. https://urn.nsk.hr/urn:nbn:hr:168:295015

Krpelnik, Ivan. "Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja." Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2018. https://urn.nsk.hr/urn:nbn:hr:168:295015

Krpelnik, I. (2018). 'Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja', Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 28 July 2024, https://urn.nsk.hr/urn:nbn:hr:168:295015

Krpelnik I. Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja [Master's thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2018 [cited 2024 July 28] Available at: https://urn.nsk.hr/urn:nbn:hr:168:295015

I. Krpelnik, "Popunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja", Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2018. Available at: https://urn.nsk.hr/urn:nbn:hr:168:295015

Metadata
TitlePopunjavanje rupa sastavljenih genoma pomoću dugačkih očitanja
Title (english)Scaffolding Assembled Genomes with Long Reads
AuthorIvan Krpelnik
MentorMile Šikić (mentor)
Committee memberMile Šikić (predsjednik povjerenstva)
Committee memberDamir Seršić (član povjerenstva)
Committee memberKrešimir Križanović (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2018-07-05, 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
Keywords (english)
Languageenglish
URN:NBNurn:nbn:hr:168:295015
Study programmeTitle: Computing
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
Type of resourceText
File originBorn digital
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Created on2019-03-13 22:01:41