De novo sastavljanje metagenoma koristeći metode za grupiranje očitanja

master's thesis

• Title (english): De Novo Metagenome Assembly Using Read Clustering
• Author: Luka Škugor
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Marko Subašić (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

Kod metagenomskog sastavljanja, suočeni smo s mnogim dodatnim izazovima u odnosu na sastavljanje jednog genoma.
U ovom radu, pokušali smo riješiti ove probleme grupiranjem segmenata koje proizvode alati treće generacije za sekvenciranje.
U idealnom slučaju, to bi omogućilo korištenje postojećih de novo alata za sastavljanje genoma na metagenomskom uzorku.
Naša implementacija grupiranja je donekle poboljšala postojeće alate za de novo sastavljanje kod primjene na metagenomskom uzorku, no još uvijek su potrebna daljnja istraživanja.
Izvorni kod rješenja dostupan je na adresi https://github.com/lukadante/rala-cluster.

Abstract (english)

Metagenomic assembly poses many additional challenges over single genome assembly.
In this work, we tried tackling these issues by clustering reads produced by third-generation sequencing tools.
In an ideal case, this would allow the use of existing de novo assembly tools for single genome assembly on metagenomic input.
Our clustering implementation showed some improvement of existing tools for de novo assembly when using them for metagenome assembly, but still requires a lot of research.
The source code of the solution is available at https://github.com/lukadante/rala-cluster.

• Keywords: metagenomsko sastavljanje; grupiranje; DNA
• Keywords (english): metagenome assembly; clustering; DNA
• Language: english
• URN:NBN: urn:nbn:hr:168:989610
• 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: 2019-03-14 01:20:47