EAGLER - Popravljanje već sastavljenih genoma koristeći dugačka očitanja

master's thesis

• Title (english): EAGLER - Eliminating Assembly Gaps by Long Read Extension
• Author: Luka Šterbić
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Damir Seršić (član povjerenstva)
• Committee member: Mirjana Domazet-Lošo (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2015-12-21, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Metode sekvenciranja druge generacije (NGS) ubrzanim tempom postaju svakodnevica kliničke medicine. Glavni nedostatak NGS tehnologija je nemogućnost rekonstrukcije dugačkih ponavljajućih regija genoma s obzirom na to da je svako pojedino očitanje dugo najviše 300 baza. EAGLER je alat namijenjen zatvaranju rupa u već sastavljenim genomima. Takvi genomi su rezultat modernih asemblera kao što su SGA, ABySS i SPAdes. Alat prima na ulaz sastavljeni genom i skup dugačkih očitanja, PacBio ili Nanopore, te kao rezultat vraća skup scaffolda. Rezultati testova na genomu Escherichia Coli K12 MG1655 pokazali su se vrlo obećavajućima. Koristeći PacBio očitanja pokrivenosti 20x postigao se prosječni identitet sekvence od 98.96%.

Abstract (english)

Next Generation Sequencing (NGS) is rapidly becoming a cornerstone of clinical medicine. The limiting factor of NGS technologies is the inability to reconstruct genomic regions with high repeat rates since a single read can span only up to 300 base pairs. The EAGLER scaffolder is a post-assembly tool aimed at closing gaps in the draft assemblies created by NGS assemblers such as SGA, ABySS and SPAdes. The scaffolder takes as input a draft genome and a set of long reads, either PacBio or Nanopore, and outputs a set of scaffolds. It has shown very promising results on the Escherichia Coli K12 MG1655 genome achieving an average identity of 98.96% using PacBio long reads with a 20x coverage.

• Keywords: Sastavljanje genoma; Metode sekvenciranje druge generacije; Dugačka očitanja; PacBio; Oxford Nanopore
• Keywords (english): Scaffolding; NGS; Long Reads; PacBio; Oxford Nanopore
• Language: english
• URN:NBN: urn:nbn:hr:168:466265
• 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: 2018-02-06 12:23:20