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master's thesis
De novo sastavljanje transkriptoma
Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing, 2015. urn:nbn:hr:168:012348
Vaser, Robert
University of Zagreb
Faculty of Electrical Engineering and Computing

Institutional repository: FER Repository

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Vaser, R. (2015). De novo sastavljanje transkriptoma (Master's thesis). Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing. Retrieved from https://urn.nsk.hr/urn:nbn:hr:168:012348

Vaser, Robert. "De novo sastavljanje transkriptoma." Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2015. https://urn.nsk.hr/urn:nbn:hr:168:012348

Vaser, Robert. "De novo sastavljanje transkriptoma." Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, 2015. https://urn.nsk.hr/urn:nbn:hr:168:012348

Vaser, R. (2015). 'De novo sastavljanje transkriptoma', Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, accessed 03 June 2024, https://urn.nsk.hr/urn:nbn:hr:168:012348

Vaser R. De novo sastavljanje transkriptoma [Master's thesis]. Zagreb: University of Zagreb, Faculty of Electrical Engineering and Computing; 2015 [cited 2024 June 03] Available at: https://urn.nsk.hr/urn:nbn:hr:168:012348

R. Vaser, "De novo sastavljanje transkriptoma", Master's thesis, University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb, 2015. Available at: https://urn.nsk.hr/urn:nbn:hr:168:012348

Metadata
TitleDe novo sastavljanje transkriptoma
Title (english)De Novo Transcriptome Assembly
AuthorRobert Vaser
MentorMile Šikić (mentor)
Committee memberMile Šikić (predsjednik povjerenstva)
Committee memberDamir Seršić (član povjerenstva)
Committee memberMladen Vučić (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Electrical Engineering and Computing
Zagreb
Defense date and country2015-07-03, Croatia
Scientific / art field,
discipline and subdiscipline		TECHNICAL SCIENCES
Computing
Abstract
U ovom radu, implementiran je de novo asembler transkriptoma koji je baziran na preklapanje-razmještaj-konsenzus paradigmi. Napisan je u programskom jeziku C++ i imenovan je Ra što je skraćeno od RNA asembler. Faza preklapanja bazirana je na poboljšanom sufiksnom polju i reproducira egzaktna preklapanja između ulaznih očitanja. Faza razmještaja koristi nekoliko metoda za pojednostavljenje grafova koji su izgrađeni nad očitanjima i njihovim preklapanjima. Kako faza preklapanja pronalazi samo egzaktne parove, trenutno ne postoji potreba za fazom konsenzusa ali ona je svejedno dio implementacije i bazirana je na partial order alignment algoritmu. Provedeni testovi upućuju da su Ra asembleru potrebna dodatna poboljšanja kako bi mogao konkurirati drugim asemblerima transkriptoma. Izvorni kod dostupan je na https://github.com/rvaser/ra.
Abstract (english)
In this thesis, a de novo transcriptome assembler was implemented based on the overlap-layout-consensus paradigm. It was written in the C++ programming language and was named Ra which is short for RNA assembler. Its overlap phase relies on the enhanced suffix arrays and reproduces exact overlaps between input reads. The layout phase uses several methods for graph simplification which includes trimming and bubble popping. Due to the exact overlap phase there is no need for a consensus phase at this moment but there exists one which is based on the partial order alignment algorithm. Conducted tests have shown that Ra needs improvements to compete with other transcriptome assemblers. Source code is available at https://github.com/rvaser/ra.
Keywords
Keywords (english)
Languageenglish
URN:NBNurn:nbn:hr:168:012348
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 on2018-02-06 14:16:01