Hibridni pristup kod sastavljanja genoma de novo

undergraduate thesis

• Title (english): Hybrid de novo genome assembly
• Author: Marko Franjić
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (predsjednik povjerenstva)
• Committee member: Mario Brčić (član povjerenstva)
• Committee member: Marina Ptiček (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2016-07-11, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Slaganje genoma postupak je kojim se bavi interdisciplinarna disciplina bioinformatika. Glavni koraci su sekvenciranje genoma u očitanja, algoritamska razrada problema, asembliranje te obrada dobivenih podataka.
U radu se izrađuje programsko rješenje koje nastoji prikazati postupak hibridnog sastavljanja genoma od samih generiranja očitanja, preko njihove algoritamske obrade, pa sve do asembliranja u jedan niz. Početna se očitanja virtualno generiraju po uzoru na dvije suvremene tehnologije, Oxford Nanopore MinION te Illumina. Dodatno, u drugom djelu rada provodi se statistička analiza koja rezultira optimalnim parametrima korištenja programa.
Na kraju su objašnjene sličnosti i razlike između ovog programskog rješenja i programa NaS koji se temelji na istom hibridnom de novo principu sastavljanja genoma.

Abstract (english)

Genome assembly is a procedure that is being developed and researched by an interdisciplinary field called bioinformatics. Main parts of the assembly are genome sequencing, using the reconstruction algorithms, reconstruction to a goal sequence and
the analysis of the results.
As a part of the thesis, the software solution attempts to demonstrate a procedure of hybrid reconstruction of genome from the very first generated genome reads to a complete assembly of a goal string. Original genome reads which are used in the process of assembly are being virtually generated to represent the reads one would acquire while using two different modern sequencing technologies, Oxford Nanopore MinION and Illumina. Furthermore, the result analysis is being covered in the second part of the thesis which gives optimal parameters that are being used in the software solution.
At the end, the crucial similarities and differences are being explained between this solution and program called NaS which is based on the same hybrid de novo genome assembly principle.

• Keywords: genom; hibridno sastavljanje; sekvenciranje; očitanja; korijenska očitanja; regrutiranje očitanja; asembliranje; statistička analiza
• Keywords (english): genome; hybrid assembly; sequencing; reads; seed-reads; reads recruitment; sequence assembly; statistical analysis
• Language: croatian
• URN:NBN: urn:nbn:hr:168:893975
• 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: 2018-02-06 08:46:22