Naslov
Scaffolding Assembled Genomes with Long Reads

Autori
Krpelnik, Ivan

Vrsta, podvrsta i kategorija rada
Ocjenski radovi, diplomski rad

Fakultet
Fakultet Elektrotehnike i Računarstva

Mjesto
Zagreb

Datum
05.07

Godina
2018

Stranica
44

Mentor
Šikić, Mile

Ključne riječi
Scaffolding, Assembly, Assemblies, Genome, Long reads

Sažetak
In this thesis, a tool for contig extension and gap closing was implemented in C++. The tool is named Ezra and could be used for extension and bridging by de novo assembler Rala. The extension and bridging methods are meant to be run in iterations, repeating the process while it produces valid extensions and bridges. The tool was tested on artificial fragments made by randomly cutting e. coli genome and on fragmented assembly produced by Rala on Pacbio bacterial datasets. The results show that this method is valid for reducing the number of contigs produced by Rala. The source code is available at https://gitlab.com/Krpa/ezra.

Izvorni jezik
Engleski

Znanstvena područja
Računarstvo

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