Struktura podataka za efikasno spremanje očitanja dobivenih sekvenciranjem genoma

undergraduate thesis

• Title (english): Data Structure for Efficient Storage of Genome Sequencing Data
• Author: Ivan Klabučar
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Josip Marić (član povjerenstva)
• Committee member: Filip Bosnić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2021-07-02, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Zbog golemih duljina genoma, njihova bilo kakva bioinformatička obrada vrlo je memorijski zahtjevna. Općenito, efikasna pohrana ocjena kvaliteta (engl. Phred quality scores) u radnu memoriju predstavlja veći izazov od pohrane samih sljedova pa se prirodno nameće pitanje njihove kompresije. U ovom radu predstavljamo algoritam kompresije ocjena kvaliteta genetskih sljedova koji smanjuje memoriju potrebnu za njihovu pohranu gotovo pa četiri puta. To postiže sažimanjem svake ocjene kvalitete s dva bita umjesto osam te računanjem povoljnog preslikavanja dvobitnih kôdova natrag u ocjene kvalitete.
Također u radu ispitujemo količinu informacije koju kompresija gubi nad stvarnim i simuliranim podatcima te utjecaj njene primjene na točnost alata Racon.

Abstract (english)

Due to the tremendous lengths of nearly all genomes, any computational attempt at their analysis is bound to be very memory intensive. Generally, Phred quality scores prove to be more difficult to store efficiently than genetic sequences, making them prime candidates for compression. This paper presents one such compression algorithm that reduces storage needed for Phred quality scores almost four times. This is achieved by using two bits, for representing a single quality score, instead of eight and by calculating satisfactory mappings of two-bit codes to quality scores.
Furthermore, we determine the amount of information lost by our algorithm and how this affects the accuracy of the tool Racon.

• Keywords: bioinformatika; ocjena kvalitete; kompresija; sažimanje; FASTQ format
• Keywords (english): bioinformatics; Phred quality scores; compression; FASTQ format
• Language: croatian
• URN:NBN: urn:nbn:hr:168:723311
• 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: 2023-01-14 20:46:43