Klasifikacija metagenomskog uzorka pomoću alata za mapiranje

undergraduate thesis

• Title (english): Metagenomic sample classification using mapping tools
• Author: Tea Madžarac
• Mentor: Krešimir Križanović (mentor)
• Committee member: Krešimir Križanović (predsjednik povjerenstva)
• Committee member: Josipa Lipovac (član povjerenstva)
• Committee member: Filip Tomas (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2023-07-05, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Metagenomika je relativno nova grana bioinformatike koja se bavi proučavanjem genetskih uzoraka prikupljenih direktno iz okoliša te nam nudi mogućnost primjene stečenog znanja u mnogim područjima, među kojima su medicina, agrikultura i ekologija. Jedan od osnovnih koraka u analizi metagenomskog uzorka je određivanje organizama koji se u njemu nalaze te njihove zastupljenosti u uzorku. Iz toga razloga važno je koristiti dobre alate za klasifikaciju. Ovaj rad bavi se osmišljavanjem algoritma koji na temelju mapiranja pokušava odrediti sastav uzorka. Pomoću alata Kraken2 izgradile su se dvije baze bakterija te se na njih mapiraju očitanja korištenjem alata minimap2. Nad dobivenim mapiranjima provela se klasifikacija pomoću osmišljenog algoritma te su dobiveni rezultati uspoređeni s rezultatima klasifikacije dobivenim uporabom alata Kraken2.

Abstract (english)

Metagenomics is a relatively new branch of bioinformatics that focuses on studying genetic samples collected directly from the environment. It has potential to be used to improve various fields, such as medicine, agriculture and ecology. One of the fundamental steps in analyzing a metagenomic samlple is determining the organisms present in the sample. Therefore, it is important to use reliable classification tools. This paper involves the development o fan algorithm that utilizes mapping to determine the composition of a sample. First, two custom bacterial databases we constructed using the Kraken 2 tool, and the reads were mapped onto these databases using the tool Minimap 2. Classification was performed based on the generated mappings using the developed algorithm, and the results were compared with the classification results obtained using the Kraken2 tool.

• Keywords: metagenomika; klasifikacija; mapiranje; Kraken 2; Minimap 2
• Keywords (english): metagenomics; classification; mapping; Kraken 2; Minimap 2
• Language: croatian
• URN:NBN: urn:nbn:hr:168:418183
• 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: 2023-07-13 10:17:18