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Scaffolding Assembled Genomes with Long Reads (CROSBI ID 420679)

Ocjenski rad | diplomski rad

Krpelnik, Ivan Scaffolding Assembled Genomes with Long Reads / Šikić, Mile (mentor); Zagreb, Fakultet elektrotehnike i računarstva, . 2018

Podaci o odgovornosti

Krpelnik, Ivan

Šikić, Mile

engleski

Scaffolding Assembled Genomes with Long Reads

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.

Scaffolding, Assembly, Assemblies, Genome, Long reads

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Podaci o izdanju

44

05.07.2018.

obranjeno

Podaci o ustanovi koja je dodijelila akademski stupanj

Fakultet elektrotehnike i računarstva

Zagreb

Povezanost rada

Računarstvo